Starting phenix.real_space_refine on Tue Apr 16 06:32:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p6k_13230/04_2024/7p6k_13230.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p6k_13230/04_2024/7p6k_13230.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p6k_13230/04_2024/7p6k_13230.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p6k_13230/04_2024/7p6k_13230.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p6k_13230/04_2024/7p6k_13230.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p6k_13230/04_2024/7p6k_13230.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 162 5.16 5 C 24729 2.51 5 N 6426 2.21 5 O 6789 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 300": "OE1" <-> "OE2" Residue "A TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 300": "OE1" <-> "OE2" Residue "C TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 699": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 653": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 38106 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 5922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5922 Classifications: {'peptide': 718} Link IDs: {'PTRANS': 27, 'TRANS': 690} Chain breaks: 2 Chain: "B" Number of atoms: 5922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5922 Classifications: {'peptide': 718} Link IDs: {'PTRANS': 27, 'TRANS': 690} Chain breaks: 2 Chain: "C" Number of atoms: 5922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5922 Classifications: {'peptide': 718} Link IDs: {'PTRANS': 27, 'TRANS': 690} Chain breaks: 2 Chain: "D" Number of atoms: 5922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5922 Classifications: {'peptide': 718} Link IDs: {'PTRANS': 27, 'TRANS': 690} Chain breaks: 2 Chain: "E" Number of atoms: 5922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5922 Classifications: {'peptide': 718} Link IDs: {'PTRANS': 27, 'TRANS': 690} Chain breaks: 2 Chain: "F" Number of atoms: 5922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5922 Classifications: {'peptide': 718} Link IDs: {'PTRANS': 27, 'TRANS': 690} Chain breaks: 2 Chain: "I" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 858 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "G" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 858 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "H" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 858 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Time building chain proxies: 19.47, per 1000 atoms: 0.51 Number of scatterers: 38106 At special positions: 0 Unit cell: (152.334, 144.522, 191.394, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 162 16.00 O 6789 8.00 N 6426 7.00 C 24729 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 310 " distance=2.03 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 65 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 295 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 310 " distance=2.03 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 65 " distance=2.03 Simple disulfide: pdb=" SG CYS B 113 " - pdb=" SG CYS B 295 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 310 " distance=2.03 Simple disulfide: pdb=" SG CYS C 57 " - pdb=" SG CYS C 65 " distance=2.03 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 295 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 310 " distance=2.03 Simple disulfide: pdb=" SG CYS D 57 " - pdb=" SG CYS D 65 " distance=2.03 Simple disulfide: pdb=" SG CYS D 113 " - pdb=" SG CYS D 295 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 310 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 65 " distance=2.03 Simple disulfide: pdb=" SG CYS E 113 " - pdb=" SG CYS E 295 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 310 " distance=2.03 Simple disulfide: pdb=" SG CYS F 57 " - pdb=" SG CYS F 65 " distance=2.03 Simple disulfide: pdb=" SG CYS F 113 " - pdb=" SG CYS F 295 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 16.20 Conformation dependent library (CDL) restraints added in 6.3 seconds 9216 Ramachandran restraints generated. 4608 Oldfield, 0 Emsley, 4608 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8964 Finding SS restraints... Secondary structure from input PDB file: 196 helices and 35 sheets defined 48.4% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.66 Creating SS restraints... Processing helix chain 'A' and resid 17 through 21 removed outlier: 3.934A pdb=" N LEU A 20 " --> pdb=" O TYR A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 49 Processing helix chain 'A' and resid 102 through 116 Processing helix chain 'A' and resid 119 through 146 Proline residue: A 126 - end of helix removed outlier: 4.878A pdb=" N TRP A 143 " --> pdb=" O CYS A 139 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N PHE A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 165 removed outlier: 3.590A pdb=" N LYS A 152 " --> pdb=" O ARG A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 176 removed outlier: 3.750A pdb=" N THR A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR A 176 " --> pdb=" O ALA A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 255 removed outlier: 3.558A pdb=" N GLY A 237 " --> pdb=" O ASP A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 286 Processing helix chain 'A' and resid 287 through 289 No H-bonds generated for 'chain 'A' and resid 287 through 289' Processing helix chain 'A' and resid 314 through 344 Processing helix chain 'A' and resid 355 through 360 Processing helix chain 'A' and resid 372 through 383 Processing helix chain 'A' and resid 383 through 392 removed outlier: 4.555A pdb=" N SER A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N VAL A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 411 removed outlier: 3.502A pdb=" N GLU A 399 " --> pdb=" O SER A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 420 Processing helix chain 'A' and resid 439 through 445 removed outlier: 3.908A pdb=" N LEU A 445 " --> pdb=" O VAL A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 468 removed outlier: 3.558A pdb=" N ILE A 465 " --> pdb=" O PRO A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 492 Processing helix chain 'A' and resid 510 through 515 removed outlier: 3.782A pdb=" N TYR A 513 " --> pdb=" O LEU A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 543 removed outlier: 4.258A pdb=" N GLY A 539 " --> pdb=" O VAL A 536 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ARG A 541 " --> pdb=" O ASP A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 566 Processing helix chain 'A' and resid 607 through 613 removed outlier: 3.616A pdb=" N ILE A 610 " --> pdb=" O PRO A 607 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER A 612 " --> pdb=" O SER A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 638 Processing helix chain 'A' and resid 655 through 661 Processing helix chain 'A' and resid 678 through 684 Processing helix chain 'A' and resid 701 through 707 removed outlier: 3.641A pdb=" N GLY A 705 " --> pdb=" O ALA A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 730 Processing helix chain 'A' and resid 747 through 753 removed outlier: 3.644A pdb=" N GLY A 751 " --> pdb=" O SER A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 776 removed outlier: 3.958A pdb=" N CYS A 776 " --> pdb=" O LEU A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 792 Processing helix chain 'A' and resid 795 through 808 removed outlier: 3.503A pdb=" N GLU A 808 " --> pdb=" O ARG A 804 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 21 removed outlier: 4.340A pdb=" N ILE B 19 " --> pdb=" O ALA B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 49 Processing helix chain 'B' and resid 102 through 117 Processing helix chain 'B' and resid 119 through 141 Proline residue: B 126 - end of helix Processing helix chain 'B' and resid 141 through 146 Processing helix chain 'B' and resid 146 through 166 removed outlier: 4.080A pdb=" N LYS B 152 " --> pdb=" O ARG B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 176 removed outlier: 4.246A pdb=" N THR B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR B 176 " --> pdb=" O ALA B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 256 removed outlier: 4.006A pdb=" N GLU B 256 " --> pdb=" O THR B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 286 Processing helix chain 'B' and resid 287 through 289 No H-bonds generated for 'chain 'B' and resid 287 through 289' Processing helix chain 'B' and resid 314 through 344 Processing helix chain 'B' and resid 354 through 360 Processing helix chain 'B' and resid 372 through 383 Processing helix chain 'B' and resid 383 through 392 removed outlier: 4.031A pdb=" N SER B 387 " --> pdb=" O ASP B 383 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N VAL B 392 " --> pdb=" O LYS B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 395 No H-bonds generated for 'chain 'B' and resid 393 through 395' Processing helix chain 'B' and resid 397 through 411 removed outlier: 3.568A pdb=" N TRP B 411 " --> pdb=" O LEU B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 419 Processing helix chain 'B' and resid 439 through 443 Processing helix chain 'B' and resid 462 through 468 Processing helix chain 'B' and resid 484 through 495 Processing helix chain 'B' and resid 504 through 508 Processing helix chain 'B' and resid 509 through 515 removed outlier: 4.030A pdb=" N TYR B 513 " --> pdb=" O LEU B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 543 Processing helix chain 'B' and resid 559 through 566 Processing helix chain 'B' and resid 629 through 638 removed outlier: 3.563A pdb=" N HIS B 637 " --> pdb=" O SER B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 661 removed outlier: 3.696A pdb=" N GLY B 659 " --> pdb=" O ILE B 656 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU B 661 " --> pdb=" O ILE B 658 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 684 removed outlier: 3.571A pdb=" N CYS B 684 " --> pdb=" O LEU B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 707 removed outlier: 3.575A pdb=" N GLY B 705 " --> pdb=" O ALA B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 730 Processing helix chain 'B' and resid 747 through 753 removed outlier: 3.623A pdb=" N VAL B 750 " --> pdb=" O PRO B 747 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY B 751 " --> pdb=" O SER B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 776 removed outlier: 4.051A pdb=" N CYS B 776 " --> pdb=" O LEU B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 792 Processing helix chain 'B' and resid 795 through 808 Processing helix chain 'C' and resid 16 through 21 removed outlier: 4.081A pdb=" N ILE C 19 " --> pdb=" O ALA C 16 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU C 20 " --> pdb=" O TYR C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 49 Processing helix chain 'C' and resid 102 through 116 Processing helix chain 'C' and resid 119 through 146 Proline residue: C 126 - end of helix removed outlier: 4.787A pdb=" N TRP C 143 " --> pdb=" O CYS C 139 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N PHE C 144 " --> pdb=" O SER C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 166 removed outlier: 4.074A pdb=" N LYS C 152 " --> pdb=" O ARG C 148 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER C 166 " --> pdb=" O LYS C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 176 removed outlier: 3.843A pdb=" N THR C 170 " --> pdb=" O SER C 166 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR C 176 " --> pdb=" O ALA C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 255 removed outlier: 3.595A pdb=" N GLY C 237 " --> pdb=" O ASP C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 286 Processing helix chain 'C' and resid 287 through 289 No H-bonds generated for 'chain 'C' and resid 287 through 289' Processing helix chain 'C' and resid 314 through 344 Processing helix chain 'C' and resid 355 through 360 Processing helix chain 'C' and resid 372 through 383 Processing helix chain 'C' and resid 383 through 392 removed outlier: 4.541A pdb=" N SER C 387 " --> pdb=" O ASP C 383 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N VAL C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 411 Processing helix chain 'C' and resid 412 through 419 Processing helix chain 'C' and resid 439 through 445 removed outlier: 3.841A pdb=" N LEU C 445 " --> pdb=" O VAL C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 468 removed outlier: 3.557A pdb=" N ILE C 465 " --> pdb=" O PRO C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 484 through 492 Processing helix chain 'C' and resid 510 through 515 removed outlier: 3.768A pdb=" N TYR C 513 " --> pdb=" O LEU C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 543 removed outlier: 4.109A pdb=" N GLY C 539 " --> pdb=" O VAL C 536 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG C 541 " --> pdb=" O ASP C 538 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU C 543 " --> pdb=" O LEU C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 566 removed outlier: 3.541A pdb=" N THR C 563 " --> pdb=" O PRO C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 613 removed outlier: 3.560A pdb=" N ILE C 610 " --> pdb=" O PRO C 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 638 Processing helix chain 'C' and resid 655 through 661 Processing helix chain 'C' and resid 678 through 684 Processing helix chain 'C' and resid 701 through 707 removed outlier: 3.503A pdb=" N ILE C 704 " --> pdb=" O PRO C 701 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY C 705 " --> pdb=" O ALA C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 724 through 730 removed outlier: 3.576A pdb=" N LEU C 727 " --> pdb=" O PRO C 724 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 753 removed outlier: 3.791A pdb=" N GLY C 751 " --> pdb=" O SER C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 770 through 776 removed outlier: 3.705A pdb=" N CYS C 776 " --> pdb=" O LEU C 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 787 through 792 Processing helix chain 'C' and resid 795 through 808 Processing helix chain 'D' and resid 15 through 21 removed outlier: 4.271A pdb=" N ILE D 19 " --> pdb=" O ALA D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 49 Processing helix chain 'D' and resid 102 through 117 Processing helix chain 'D' and resid 119 through 141 Proline residue: D 126 - end of helix Processing helix chain 'D' and resid 141 through 146 Processing helix chain 'D' and resid 146 through 166 removed outlier: 4.248A pdb=" N LYS D 152 " --> pdb=" O ARG D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 176 removed outlier: 4.319A pdb=" N THR D 170 " --> pdb=" O SER D 166 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG D 171 " --> pdb=" O PRO D 167 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR D 176 " --> pdb=" O ALA D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 256 removed outlier: 4.040A pdb=" N GLU D 256 " --> pdb=" O THR D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 286 Processing helix chain 'D' and resid 287 through 289 No H-bonds generated for 'chain 'D' and resid 287 through 289' Processing helix chain 'D' and resid 314 through 344 Processing helix chain 'D' and resid 354 through 360 removed outlier: 3.857A pdb=" N SER D 360 " --> pdb=" O ILE D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 383 Processing helix chain 'D' and resid 383 through 392 removed outlier: 4.032A pdb=" N SER D 387 " --> pdb=" O ASP D 383 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL D 392 " --> pdb=" O LYS D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 411 Processing helix chain 'D' and resid 412 through 419 Processing helix chain 'D' and resid 439 through 444 Processing helix chain 'D' and resid 462 through 468 Processing helix chain 'D' and resid 484 through 495 Processing helix chain 'D' and resid 504 through 508 Processing helix chain 'D' and resid 511 through 515 removed outlier: 3.737A pdb=" N LEU D 515 " --> pdb=" O ILE D 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 543 removed outlier: 4.362A pdb=" N ARG D 541 " --> pdb=" O ASP D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 566 Processing helix chain 'D' and resid 567 through 569 No H-bonds generated for 'chain 'D' and resid 567 through 569' Processing helix chain 'D' and resid 629 through 638 removed outlier: 3.631A pdb=" N ILE D 632 " --> pdb=" O ILE D 629 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN D 636 " --> pdb=" O ILE D 633 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N HIS D 637 " --> pdb=" O SER D 634 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 660 removed outlier: 3.649A pdb=" N GLY D 659 " --> pdb=" O ILE D 656 " (cutoff:3.500A) Processing helix chain 'D' and resid 680 through 684 removed outlier: 3.641A pdb=" N CYS D 684 " --> pdb=" O LEU D 681 " (cutoff:3.500A) Processing helix chain 'D' and resid 701 through 707 Processing helix chain 'D' and resid 724 through 730 Processing helix chain 'D' and resid 747 through 753 Processing helix chain 'D' and resid 770 through 776 removed outlier: 4.096A pdb=" N CYS D 776 " --> pdb=" O LEU D 773 " (cutoff:3.500A) Processing helix chain 'D' and resid 787 through 792 Processing helix chain 'D' and resid 795 through 808 Processing helix chain 'E' and resid 17 through 21 removed outlier: 3.743A pdb=" N LEU E 20 " --> pdb=" O TYR E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 49 Processing helix chain 'E' and resid 102 through 117 Processing helix chain 'E' and resid 119 through 146 Proline residue: E 126 - end of helix removed outlier: 4.757A pdb=" N TRP E 143 " --> pdb=" O CYS E 139 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N PHE E 144 " --> pdb=" O SER E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 166 removed outlier: 4.174A pdb=" N LYS E 152 " --> pdb=" O ARG E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 176 removed outlier: 3.931A pdb=" N THR E 170 " --> pdb=" O SER E 166 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR E 176 " --> pdb=" O ALA E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 255 removed outlier: 3.562A pdb=" N GLY E 237 " --> pdb=" O ASP E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 286 Processing helix chain 'E' and resid 287 through 289 No H-bonds generated for 'chain 'E' and resid 287 through 289' Processing helix chain 'E' and resid 314 through 344 Processing helix chain 'E' and resid 355 through 360 Processing helix chain 'E' and resid 372 through 383 Processing helix chain 'E' and resid 383 through 392 removed outlier: 4.535A pdb=" N SER E 387 " --> pdb=" O ASP E 383 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N VAL E 392 " --> pdb=" O LYS E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 411 Processing helix chain 'E' and resid 412 through 420 Processing helix chain 'E' and resid 439 through 444 Processing helix chain 'E' and resid 462 through 468 Processing helix chain 'E' and resid 484 through 492 Processing helix chain 'E' and resid 504 through 508 removed outlier: 3.648A pdb=" N GLU E 507 " --> pdb=" O ASP E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 510 through 515 removed outlier: 3.902A pdb=" N TYR E 513 " --> pdb=" O LEU E 510 " (cutoff:3.500A) Processing helix chain 'E' and resid 535 through 543 removed outlier: 4.244A pdb=" N GLY E 539 " --> pdb=" O VAL E 536 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG E 541 " --> pdb=" O ASP E 538 " (cutoff:3.500A) Processing helix chain 'E' and resid 559 through 566 Processing helix chain 'E' and resid 607 through 611 removed outlier: 3.530A pdb=" N ILE E 610 " --> pdb=" O PRO E 607 " (cutoff:3.500A) Processing helix chain 'E' and resid 631 through 636 Processing helix chain 'E' and resid 655 through 660 Processing helix chain 'E' and resid 678 through 684 Processing helix chain 'E' and resid 701 through 707 removed outlier: 3.914A pdb=" N GLY E 705 " --> pdb=" O ALA E 702 " (cutoff:3.500A) Processing helix chain 'E' and resid 725 through 730 Processing helix chain 'E' and resid 747 through 753 removed outlier: 3.579A pdb=" N VAL E 750 " --> pdb=" O PRO E 747 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY E 751 " --> pdb=" O SER E 748 " (cutoff:3.500A) Processing helix chain 'E' and resid 771 through 776 removed outlier: 3.745A pdb=" N GLY E 774 " --> pdb=" O VAL E 771 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N CYS E 776 " --> pdb=" O LEU E 773 " (cutoff:3.500A) Processing helix chain 'E' and resid 787 through 793 Processing helix chain 'E' and resid 795 through 808 Processing helix chain 'F' and resid 17 through 21 Processing helix chain 'F' and resid 22 through 49 Processing helix chain 'F' and resid 102 through 117 Processing helix chain 'F' and resid 119 through 146 Proline residue: F 126 - end of helix removed outlier: 4.819A pdb=" N TRP F 143 " --> pdb=" O CYS F 139 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N PHE F 144 " --> pdb=" O SER F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 166 removed outlier: 4.686A pdb=" N LYS F 152 " --> pdb=" O ARG F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 176 removed outlier: 3.589A pdb=" N THR F 176 " --> pdb=" O ALA F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 255 Processing helix chain 'F' and resid 259 through 286 Processing helix chain 'F' and resid 287 through 289 No H-bonds generated for 'chain 'F' and resid 287 through 289' Processing helix chain 'F' and resid 314 through 344 Processing helix chain 'F' and resid 353 through 360 removed outlier: 3.533A pdb=" N ARG F 357 " --> pdb=" O PHE F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 383 Processing helix chain 'F' and resid 383 through 392 removed outlier: 4.124A pdb=" N SER F 387 " --> pdb=" O ASP F 383 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL F 392 " --> pdb=" O LYS F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 411 Processing helix chain 'F' and resid 412 through 419 Processing helix chain 'F' and resid 439 through 445 removed outlier: 3.576A pdb=" N VAL F 442 " --> pdb=" O PRO F 439 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU F 445 " --> pdb=" O VAL F 442 " (cutoff:3.500A) Processing helix chain 'F' and resid 462 through 468 Processing helix chain 'F' and resid 484 through 495 Processing helix chain 'F' and resid 504 through 508 Processing helix chain 'F' and resid 509 through 513 removed outlier: 3.757A pdb=" N ILE F 512 " --> pdb=" O PRO F 509 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TYR F 513 " --> pdb=" O LEU F 510 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 509 through 513' Processing helix chain 'F' and resid 537 through 543 removed outlier: 3.563A pdb=" N LEU F 540 " --> pdb=" O ILE F 537 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG F 541 " --> pdb=" O ASP F 538 " (cutoff:3.500A) Processing helix chain 'F' and resid 559 through 566 Processing helix chain 'F' and resid 607 through 613 removed outlier: 3.624A pdb=" N ILE F 610 " --> pdb=" O PRO F 607 " (cutoff:3.500A) Processing helix chain 'F' and resid 629 through 638 removed outlier: 3.565A pdb=" N HIS F 637 " --> pdb=" O SER F 634 " (cutoff:3.500A) Processing helix chain 'F' and resid 655 through 661 removed outlier: 3.852A pdb=" N GLY F 659 " --> pdb=" O ILE F 656 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU F 661 " --> pdb=" O ILE F 658 " (cutoff:3.500A) Processing helix chain 'F' and resid 678 through 684 removed outlier: 3.699A pdb=" N LEU F 681 " --> pdb=" O PRO F 678 " (cutoff:3.500A) Processing helix chain 'F' and resid 701 through 707 removed outlier: 3.730A pdb=" N ILE F 704 " --> pdb=" O PRO F 701 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY F 705 " --> pdb=" O ALA F 702 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU F 707 " --> pdb=" O ILE F 704 " (cutoff:3.500A) Processing helix chain 'F' and resid 724 through 730 Processing helix chain 'F' and resid 747 through 753 removed outlier: 3.544A pdb=" N GLY F 751 " --> pdb=" O SER F 748 " (cutoff:3.500A) Processing helix chain 'F' and resid 770 through 776 removed outlier: 3.768A pdb=" N CYS F 776 " --> pdb=" O LEU F 773 " (cutoff:3.500A) Processing helix chain 'F' and resid 787 through 793 Processing helix chain 'F' and resid 795 through 808 Processing helix chain 'I' and resid 62 through 65 Processing helix chain 'G' and resid 62 through 65 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.234A pdb=" N THR H 91 " --> pdb=" O PRO H 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AA2, first strand: chain 'A' and resid 421 through 422 removed outlier: 6.564A pdb=" N LEU A 428 " --> pdb=" O VAL A 450 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N LYS A 452 " --> pdb=" O LEU A 428 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU A 430 " --> pdb=" O LYS A 452 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N GLU A 454 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LEU A 432 " --> pdb=" O GLU A 454 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LEU A 451 " --> pdb=" O TRP A 475 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N TYR A 477 " --> pdb=" O LEU A 451 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU A 453 " --> pdb=" O TYR A 477 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU A 498 " --> pdb=" O HIS A 522 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N THR A 524 " --> pdb=" O LEU A 498 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE A 500 " --> pdb=" O THR A 524 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LEU A 521 " --> pdb=" O ARG A 550 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N LYS A 552 " --> pdb=" O LEU A 521 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU A 523 " --> pdb=" O LYS A 552 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N LEU A 572 " --> pdb=" O GLU A 597 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ILE A 599 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ILE A 574 " --> pdb=" O ILE A 599 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ILE A 619 " --> pdb=" O LYS A 645 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LEU A 644 " --> pdb=" O TYR A 668 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU A 760 " --> pdb=" O LEU A 736 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ILE A 759 " --> pdb=" O VAL A 785 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 459 through 461 Processing sheet with id=AA4, first strand: chain 'B' and resid 53 through 56 Processing sheet with id=AA5, first strand: chain 'B' and resid 60 through 61 Processing sheet with id=AA6, first strand: chain 'B' and resid 421 through 422 removed outlier: 6.985A pdb=" N LEU B 498 " --> pdb=" O HIS B 522 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N THR B 524 " --> pdb=" O LEU B 498 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ILE B 500 " --> pdb=" O THR B 524 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU B 521 " --> pdb=" O ARG B 550 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N LYS B 552 " --> pdb=" O LEU B 521 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU B 523 " --> pdb=" O LYS B 552 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU B 596 " --> pdb=" O GLU B 618 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 460 through 461 Processing sheet with id=AA8, first strand: chain 'B' and resid 643 through 645 removed outlier: 3.776A pdb=" N TYR B 668 " --> pdb=" O LEU B 644 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ILE B 759 " --> pdb=" O VAL B 785 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 53 through 56 Processing sheet with id=AB1, first strand: chain 'C' and resid 421 through 422 removed outlier: 6.162A pdb=" N LEU C 428 " --> pdb=" O VAL C 450 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N LYS C 452 " --> pdb=" O LEU C 428 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU C 430 " --> pdb=" O LYS C 452 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N GLU C 454 " --> pdb=" O LEU C 430 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N LEU C 432 " --> pdb=" O GLU C 454 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N LEU C 572 " --> pdb=" O GLU C 597 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ILE C 599 " --> pdb=" O LEU C 572 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ILE C 574 " --> pdb=" O ILE C 599 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU C 644 " --> pdb=" O ARG C 666 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR C 668 " --> pdb=" O LEU C 644 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU C 760 " --> pdb=" O LEU C 736 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE C 759 " --> pdb=" O VAL C 785 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 459 through 461 Processing sheet with id=AB3, first strand: chain 'D' and resid 53 through 56 Processing sheet with id=AB4, first strand: chain 'D' and resid 60 through 61 removed outlier: 3.712A pdb=" N THR D 61 " --> pdb=" O SER D 64 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 420 through 422 removed outlier: 6.403A pdb=" N LEU D 428 " --> pdb=" O VAL D 450 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N LYS D 452 " --> pdb=" O LEU D 428 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU D 430 " --> pdb=" O LYS D 452 " (cutoff:3.500A) removed outlier: 8.439A pdb=" N GLU D 454 " --> pdb=" O LEU D 430 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N LEU D 432 " --> pdb=" O GLU D 454 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N LEU D 498 " --> pdb=" O HIS D 522 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N THR D 524 " --> pdb=" O LEU D 498 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE D 500 " --> pdb=" O THR D 524 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU D 549 " --> pdb=" O SER D 573 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ASN D 575 " --> pdb=" O LEU D 549 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU D 551 " --> pdb=" O ASN D 575 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU D 596 " --> pdb=" O GLU D 618 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP D 620 " --> pdb=" O LEU D 596 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ILE D 619 " --> pdb=" O LYS D 645 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP D 691 " --> pdb=" O LEU D 667 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 459 through 461 Processing sheet with id=AB7, first strand: chain 'D' and resid 712 through 714 removed outlier: 6.627A pdb=" N LEU D 713 " --> pdb=" O HIS D 737 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 53 through 56 Processing sheet with id=AB9, first strand: chain 'E' and resid 421 through 422 removed outlier: 6.469A pdb=" N LEU E 428 " --> pdb=" O VAL E 450 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N LYS E 452 " --> pdb=" O LEU E 428 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU E 430 " --> pdb=" O LYS E 452 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N GLU E 454 " --> pdb=" O LEU E 430 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N LEU E 432 " --> pdb=" O GLU E 454 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU E 451 " --> pdb=" O TRP E 475 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N TYR E 477 " --> pdb=" O LEU E 451 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU E 453 " --> pdb=" O TYR E 477 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU E 521 " --> pdb=" O ARG E 550 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N LYS E 552 " --> pdb=" O LEU E 521 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LEU E 523 " --> pdb=" O LYS E 552 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU E 572 " --> pdb=" O GLU E 597 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N ILE E 599 " --> pdb=" O LEU E 572 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ILE E 574 " --> pdb=" O ILE E 599 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE E 619 " --> pdb=" O LYS E 645 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LEU E 713 " --> pdb=" O HIS E 737 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU E 760 " --> pdb=" O LEU E 736 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ILE E 759 " --> pdb=" O VAL E 785 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 459 through 461 Processing sheet with id=AC2, first strand: chain 'F' and resid 53 through 56 Processing sheet with id=AC3, first strand: chain 'F' and resid 60 through 61 Processing sheet with id=AC4, first strand: chain 'F' and resid 420 through 422 removed outlier: 3.577A pdb=" N LYS F 452 " --> pdb=" O LEU F 430 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N LEU F 549 " --> pdb=" O SER F 573 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ASN F 575 " --> pdb=" O LEU F 549 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU F 551 " --> pdb=" O ASN F 575 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N LEU F 572 " --> pdb=" O GLU F 597 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ILE F 599 " --> pdb=" O LEU F 572 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N ILE F 574 " --> pdb=" O ILE F 599 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASP F 620 " --> pdb=" O LEU F 596 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 643 through 645 Processing sheet with id=AC6, first strand: chain 'F' and resid 689 through 691 removed outlier: 7.517A pdb=" N LEU F 690 " --> pdb=" O ALA F 714 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU F 713 " --> pdb=" O HIS F 737 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N LEU F 736 " --> pdb=" O GLU F 760 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ILE F 759 " --> pdb=" O VAL F 785 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'I' and resid 19 through 21 removed outlier: 3.526A pdb=" N THR I 78 " --> pdb=" O ASP I 73 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 46 through 47 removed outlier: 3.542A pdb=" N GLU I 46 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL I 93 " --> pdb=" O GLN I 39 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 49 through 51 removed outlier: 3.661A pdb=" N ALA I 50 " --> pdb=" O ALA I 59 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA I 59 " --> pdb=" O ALA I 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'G' and resid 19 through 21 removed outlier: 3.651A pdb=" N THR G 78 " --> pdb=" O ASP G 73 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 46 through 47 removed outlier: 3.909A pdb=" N VAL G 98 " --> pdb=" O TYR G 104 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR G 104 " --> pdb=" O VAL G 98 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 46 through 47 removed outlier: 3.536A pdb=" N TYR G 94 " --> pdb=" O THR G 109 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR G 109 " --> pdb=" O TYR G 94 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 49 through 51 removed outlier: 3.750A pdb=" N ALA G 50 " --> pdb=" O ALA G 59 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA G 59 " --> pdb=" O ALA G 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AD6, first strand: chain 'H' and resid 17 through 21 removed outlier: 3.516A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 46 through 47 removed outlier: 3.585A pdb=" N GLU H 46 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL H 93 " --> pdb=" O GLN H 39 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR H 94 " --> pdb=" O THR H 109 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N THR H 109 " --> pdb=" O TYR H 94 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 49 through 51 removed outlier: 3.882A pdb=" N ALA H 50 " --> pdb=" O ALA H 59 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA H 59 " --> pdb=" O ALA H 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 1698 hydrogen bonds defined for protein. 4311 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 17.78 Time building geometry restraints manager: 16.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 12072 1.35 - 1.46: 8743 1.46 - 1.58: 17912 1.58 - 1.70: 0 1.70 - 1.81: 222 Bond restraints: 38949 Sorted by residual: bond pdb=" C ASP C 371 " pdb=" N PHE C 372 " ideal model delta sigma weight residual 1.332 1.318 0.014 1.40e-02 5.10e+03 1.02e+00 bond pdb=" CA ILE A 606 " pdb=" CB ILE A 606 " ideal model delta sigma weight residual 1.537 1.525 0.012 1.29e-02 6.01e+03 9.04e-01 bond pdb=" N GLY G 101 " pdb=" CA GLY G 101 " ideal model delta sigma weight residual 1.449 1.463 -0.014 1.45e-02 4.76e+03 8.74e-01 bond pdb=" CA ILE A 289 " pdb=" CB ILE A 289 " ideal model delta sigma weight residual 1.527 1.539 -0.012 1.31e-02 5.83e+03 8.47e-01 bond pdb=" C ILE E 456 " pdb=" O ILE E 456 " ideal model delta sigma weight residual 1.232 1.240 -0.008 1.01e-02 9.80e+03 7.02e-01 ... (remaining 38944 not shown) Histogram of bond angle deviations from ideal: 99.83 - 106.67: 982 106.67 - 113.50: 21757 113.50 - 120.33: 14109 120.33 - 127.16: 15490 127.16 - 133.99: 456 Bond angle restraints: 52794 Sorted by residual: angle pdb=" N VAL D 742 " pdb=" CA VAL D 742 " pdb=" C VAL D 742 " ideal model delta sigma weight residual 111.77 107.78 3.99 1.04e+00 9.25e-01 1.47e+01 angle pdb=" N ILE C 259 " pdb=" CA ILE C 259 " pdb=" C ILE C 259 " ideal model delta sigma weight residual 113.71 110.29 3.42 9.50e-01 1.11e+00 1.29e+01 angle pdb=" N ILE E 259 " pdb=" CA ILE E 259 " pdb=" C ILE E 259 " ideal model delta sigma weight residual 113.53 110.22 3.31 9.80e-01 1.04e+00 1.14e+01 angle pdb=" N VAL C 446 " pdb=" CA VAL C 446 " pdb=" C VAL C 446 " ideal model delta sigma weight residual 112.80 109.18 3.62 1.15e+00 7.56e-01 9.93e+00 angle pdb=" N VAL F 536 " pdb=" CA VAL F 536 " pdb=" C VAL F 536 " ideal model delta sigma weight residual 113.07 108.79 4.28 1.37e+00 5.33e-01 9.77e+00 ... (remaining 52789 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 22166 17.79 - 35.58: 1101 35.58 - 53.37: 234 53.37 - 71.17: 44 71.17 - 88.96: 17 Dihedral angle restraints: 23562 sinusoidal: 9771 harmonic: 13791 Sorted by residual: dihedral pdb=" CB CYS F 57 " pdb=" SG CYS F 57 " pdb=" SG CYS F 65 " pdb=" CB CYS F 65 " ideal model delta sinusoidal sigma weight residual -86.00 -56.78 -29.22 1 1.00e+01 1.00e-02 1.22e+01 dihedral pdb=" CB CYS D 57 " pdb=" SG CYS D 57 " pdb=" SG CYS D 65 " pdb=" CB CYS D 65 " ideal model delta sinusoidal sigma weight residual -86.00 -58.48 -27.52 1 1.00e+01 1.00e-02 1.09e+01 dihedral pdb=" CA CYS E 730 " pdb=" C CYS E 730 " pdb=" N ARG E 731 " pdb=" CA ARG E 731 " ideal model delta harmonic sigma weight residual -180.00 -163.52 -16.48 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 23559 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 3579 0.028 - 0.057: 1749 0.057 - 0.085: 476 0.085 - 0.113: 230 0.113 - 0.142: 47 Chirality restraints: 6081 Sorted by residual: chirality pdb=" CA ILE C 677 " pdb=" N ILE C 677 " pdb=" C ILE C 677 " pdb=" CB ILE C 677 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" CA ILE B 508 " pdb=" N ILE B 508 " pdb=" C ILE B 508 " pdb=" CB ILE B 508 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.63e-01 chirality pdb=" CA VAL D 786 " pdb=" N VAL D 786 " pdb=" C VAL D 786 " pdb=" CB VAL D 786 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.61e-01 ... (remaining 6078 not shown) Planarity restraints: 6555 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE I 27 " -0.023 5.00e-02 4.00e+02 3.50e-02 1.96e+00 pdb=" N PRO I 28 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO I 28 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO I 28 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE G 27 " 0.022 5.00e-02 4.00e+02 3.32e-02 1.77e+00 pdb=" N PRO G 28 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO G 28 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO G 28 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE H 27 " 0.021 5.00e-02 4.00e+02 3.19e-02 1.63e+00 pdb=" N PRO H 28 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO H 28 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO H 28 " 0.018 5.00e-02 4.00e+02 ... (remaining 6552 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 6116 2.76 - 3.30: 38708 3.30 - 3.83: 65706 3.83 - 4.37: 76977 4.37 - 4.90: 130519 Nonbonded interactions: 318026 Sorted by model distance: nonbonded pdb=" OH TYR C 513 " pdb=" O VAL C 536 " model vdw 2.230 2.440 nonbonded pdb=" OG1 THR B 303 " pdb=" OH TYR B 308 " model vdw 2.234 2.440 nonbonded pdb=" OH TYR D 351 " pdb=" OD2 ASP D 380 " model vdw 2.234 2.440 nonbonded pdb=" OH TYR F 351 " pdb=" OD2 ASP F 380 " model vdw 2.238 2.440 nonbonded pdb=" OH TYR E 513 " pdb=" O VAL E 536 " model vdw 2.238 2.440 ... (remaining 318021 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 9.370 Check model and map are aligned: 0.520 Set scattering table: 0.350 Process input model: 99.830 Find NCS groups from input model: 2.700 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 38949 Z= 0.119 Angle : 0.469 8.745 52794 Z= 0.264 Chirality : 0.038 0.142 6081 Planarity : 0.003 0.035 6555 Dihedral : 11.363 88.958 14535 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.89 % Allowed : 7.38 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.13), residues: 4608 helix: 0.34 (0.12), residues: 2115 sheet: -0.90 (0.20), residues: 741 loop : 0.01 (0.16), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 647 HIS 0.002 0.000 HIS C 104 PHE 0.010 0.001 PHE G 27 TYR 0.013 0.001 TYR C 281 ARG 0.002 0.000 ARG E 103 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9216 Ramachandran restraints generated. 4608 Oldfield, 0 Emsley, 4608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9216 Ramachandran restraints generated. 4608 Oldfield, 0 Emsley, 4608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 400 time to evaluate : 4.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 HIS cc_start: 0.8266 (OUTLIER) cc_final: 0.7650 (t70) REVERT: A 278 ILE cc_start: 0.8148 (OUTLIER) cc_final: 0.7894 (tt) REVERT: A 353 PHE cc_start: 0.6193 (OUTLIER) cc_final: 0.5477 (m-80) REVERT: A 697 LEU cc_start: 0.7660 (mt) cc_final: 0.7373 (tp) REVERT: B 279 ILE cc_start: 0.7210 (OUTLIER) cc_final: 0.6932 (tt) REVERT: B 353 PHE cc_start: 0.6572 (OUTLIER) cc_final: 0.5811 (t80) REVERT: B 622 LYS cc_start: 0.5125 (OUTLIER) cc_final: 0.4772 (mmtm) REVERT: B 759 ILE cc_start: 0.7165 (OUTLIER) cc_final: 0.6522 (tp) REVERT: C 353 PHE cc_start: 0.6263 (OUTLIER) cc_final: 0.5222 (m-80) REVERT: D 104 HIS cc_start: 0.8412 (OUTLIER) cc_final: 0.7906 (t70) REVERT: D 293 VAL cc_start: 0.9387 (OUTLIER) cc_final: 0.9183 (p) REVERT: D 325 TYR cc_start: 0.7516 (t80) cc_final: 0.7312 (t80) REVERT: D 353 PHE cc_start: 0.5833 (OUTLIER) cc_final: 0.5113 (t80) REVERT: E 273 ILE cc_start: 0.8623 (pt) cc_final: 0.8251 (mt) REVERT: E 318 PHE cc_start: 0.8839 (OUTLIER) cc_final: 0.8520 (m-10) REVERT: E 738 LEU cc_start: 0.6573 (OUTLIER) cc_final: 0.5815 (pt) REVERT: F 353 PHE cc_start: 0.5949 (OUTLIER) cc_final: 0.5480 (t80) REVERT: F 359 GLU cc_start: 0.5275 (OUTLIER) cc_final: 0.4910 (pt0) REVERT: F 605 ARG cc_start: 0.3934 (tpp-160) cc_final: 0.3642 (ptp90) REVERT: I 45 ARG cc_start: 0.3035 (OUTLIER) cc_final: -0.0175 (mtt180) REVERT: I 58 THR cc_start: 0.6241 (t) cc_final: 0.6016 (t) REVERT: I 68 PHE cc_start: 0.2954 (OUTLIER) cc_final: 0.2370 (m-80) REVERT: I 69 THR cc_start: 0.0562 (OUTLIER) cc_final: 0.0165 (m) REVERT: G 31 GLN cc_start: 0.6546 (OUTLIER) cc_final: 0.6090 (pm20) REVERT: G 45 ARG cc_start: 0.3431 (OUTLIER) cc_final: 0.0685 (mtt180) REVERT: G 68 PHE cc_start: 0.2727 (OUTLIER) cc_final: 0.1566 (m-80) REVERT: G 69 THR cc_start: 0.1181 (OUTLIER) cc_final: 0.0887 (m) REVERT: H 11 LEU cc_start: 0.2402 (OUTLIER) cc_final: 0.2115 (tp) REVERT: H 45 ARG cc_start: 0.3640 (OUTLIER) cc_final: 0.0542 (mtp85) REVERT: H 68 PHE cc_start: 0.2495 (OUTLIER) cc_final: 0.1671 (m-80) outliers start: 166 outliers final: 39 residues processed: 550 average time/residue: 0.5217 time to fit residues: 464.3101 Evaluate side-chains 242 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 178 time to evaluate : 4.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 622 LYS Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 657 GLN Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 318 PHE Chi-restraints excluded: chain E residue 527 LEU Chi-restraints excluded: chain E residue 696 ASN Chi-restraints excluded: chain E residue 738 LEU Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 359 GLU Chi-restraints excluded: chain F residue 635 PHE Chi-restraints excluded: chain F residue 736 LEU Chi-restraints excluded: chain I residue 45 ARG Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain G residue 31 GLN Chi-restraints excluded: chain G residue 45 ARG Chi-restraints excluded: chain G residue 68 PHE Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 45 ARG Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 93 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 387 optimal weight: 3.9990 chunk 347 optimal weight: 0.4980 chunk 193 optimal weight: 10.0000 chunk 118 optimal weight: 6.9990 chunk 234 optimal weight: 3.9990 chunk 185 optimal weight: 4.9990 chunk 359 optimal weight: 1.9990 chunk 139 optimal weight: 5.9990 chunk 218 optimal weight: 10.0000 chunk 267 optimal weight: 6.9990 chunk 416 optimal weight: 1.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 696 ASN ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 526 ASN B 532 ASN B 624 ASN B 650 HIS B 695 ASN ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 HIS ** C 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 592 ASN C 617 GLN ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 381 GLN D 404 GLN D 554 ASN ** D 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 650 HIS E 105 GLN E 657 GLN ** E 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 639 HIS ** F 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 82 GLN ** G 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN H 82 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 38949 Z= 0.317 Angle : 0.611 10.431 52794 Z= 0.316 Chirality : 0.044 0.193 6081 Planarity : 0.004 0.039 6555 Dihedral : 6.228 57.970 5194 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 4.01 % Allowed : 11.20 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.13), residues: 4608 helix: 0.11 (0.12), residues: 2118 sheet: -0.92 (0.20), residues: 744 loop : -0.22 (0.16), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 647 HIS 0.009 0.001 HIS B 650 PHE 0.024 0.002 PHE A 146 TYR 0.022 0.002 TYR E 281 ARG 0.007 0.001 ARG B 640 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9216 Ramachandran restraints generated. 4608 Oldfield, 0 Emsley, 4608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9216 Ramachandran restraints generated. 4608 Oldfield, 0 Emsley, 4608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 203 time to evaluate : 4.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 HIS cc_start: 0.8644 (OUTLIER) cc_final: 0.7864 (t70) REVERT: A 269 ILE cc_start: 0.9021 (OUTLIER) cc_final: 0.8748 (mp) REVERT: A 278 ILE cc_start: 0.7978 (OUTLIER) cc_final: 0.7672 (tt) REVERT: A 353 PHE cc_start: 0.6357 (OUTLIER) cc_final: 0.4985 (m-80) REVERT: A 375 MET cc_start: 0.8150 (mpp) cc_final: 0.7942 (mpp) REVERT: A 507 GLU cc_start: 0.6136 (OUTLIER) cc_final: 0.5889 (tt0) REVERT: A 647 TRP cc_start: 0.7623 (OUTLIER) cc_final: 0.6950 (p90) REVERT: A 697 LEU cc_start: 0.7657 (mt) cc_final: 0.7381 (tp) REVERT: B 353 PHE cc_start: 0.6763 (OUTLIER) cc_final: 0.6123 (t80) REVERT: C 269 ILE cc_start: 0.9148 (OUTLIER) cc_final: 0.8872 (mm) REVERT: C 353 PHE cc_start: 0.6485 (OUTLIER) cc_final: 0.4928 (m-80) REVERT: C 375 MET cc_start: 0.8298 (mpp) cc_final: 0.8072 (mpp) REVERT: D 104 HIS cc_start: 0.8754 (OUTLIER) cc_final: 0.8432 (t70) REVERT: D 353 PHE cc_start: 0.6084 (OUTLIER) cc_final: 0.5338 (t80) REVERT: E 318 PHE cc_start: 0.8896 (OUTLIER) cc_final: 0.8546 (m-10) REVERT: E 353 PHE cc_start: 0.6223 (OUTLIER) cc_final: 0.4752 (m-80) REVERT: F 353 PHE cc_start: 0.6391 (OUTLIER) cc_final: 0.5857 (t80) REVERT: F 584 LEU cc_start: 0.2924 (OUTLIER) cc_final: 0.2013 (mt) REVERT: F 605 ARG cc_start: 0.4128 (tpp-160) cc_final: 0.3737 (ptp90) REVERT: I 45 ARG cc_start: 0.3717 (OUTLIER) cc_final: 0.0063 (mtt180) REVERT: I 68 PHE cc_start: 0.2733 (OUTLIER) cc_final: 0.1733 (m-80) REVERT: I 69 THR cc_start: 0.0750 (OUTLIER) cc_final: 0.0152 (m) REVERT: G 31 GLN cc_start: 0.6584 (OUTLIER) cc_final: 0.6073 (pm20) REVERT: G 45 ARG cc_start: 0.4212 (OUTLIER) cc_final: 0.1816 (mtt180) REVERT: G 46 GLU cc_start: 0.4091 (tp30) cc_final: 0.2656 (tt0) REVERT: G 68 PHE cc_start: 0.2677 (OUTLIER) cc_final: 0.1970 (m-80) REVERT: G 69 THR cc_start: 0.1318 (OUTLIER) cc_final: 0.0792 (m) REVERT: G 83 MET cc_start: 0.0588 (mpp) cc_final: 0.0205 (mpp) REVERT: H 11 LEU cc_start: 0.2727 (OUTLIER) cc_final: 0.2454 (tt) REVERT: H 45 ARG cc_start: 0.3464 (OUTLIER) cc_final: 0.0557 (mtp85) REVERT: H 68 PHE cc_start: 0.2902 (OUTLIER) cc_final: 0.2142 (m-80) REVERT: H 83 MET cc_start: 0.0673 (mpp) cc_final: 0.0276 (mpp) REVERT: H 102 PHE cc_start: 0.5392 (OUTLIER) cc_final: 0.4968 (t80) outliers start: 171 outliers final: 89 residues processed: 358 average time/residue: 0.4656 time to fit residues: 282.1082 Evaluate side-chains 273 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 158 time to evaluate : 4.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 647 TRP Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 622 LYS Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 617 GLN Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 771 VAL Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 274 LYS Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 318 PHE Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 503 THR Chi-restraints excluded: chain E residue 527 LEU Chi-restraints excluded: chain E residue 696 ASN Chi-restraints excluded: chain E residue 738 LEU Chi-restraints excluded: chain E residue 769 LEU Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 495 LEU Chi-restraints excluded: chain F residue 543 LEU Chi-restraints excluded: chain F residue 584 LEU Chi-restraints excluded: chain F residue 757 THR Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 45 ARG Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 62 ASP Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 73 ASP Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain G residue 31 GLN Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain G residue 45 ARG Chi-restraints excluded: chain G residue 68 PHE Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 45 ARG Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 102 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 231 optimal weight: 0.9980 chunk 129 optimal weight: 0.0370 chunk 346 optimal weight: 9.9990 chunk 283 optimal weight: 7.9990 chunk 114 optimal weight: 10.0000 chunk 417 optimal weight: 9.9990 chunk 451 optimal weight: 20.0000 chunk 371 optimal weight: 0.0170 chunk 414 optimal weight: 0.5980 chunk 142 optimal weight: 6.9990 chunk 334 optimal weight: 0.8980 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 406 ASN B 531 ASN B 617 GLN B 637 HIS B 650 HIS ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 522 HIS ** E 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 695 ASN G 31 GLN ** G 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6927 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 38949 Z= 0.139 Angle : 0.499 8.273 52794 Z= 0.256 Chirality : 0.040 0.171 6081 Planarity : 0.003 0.043 6555 Dihedral : 5.871 58.767 5179 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.54 % Allowed : 12.38 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.13), residues: 4608 helix: 0.20 (0.12), residues: 2148 sheet: -0.77 (0.21), residues: 708 loop : -0.28 (0.16), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 411 HIS 0.004 0.001 HIS E 132 PHE 0.025 0.001 PHE B 699 TYR 0.013 0.001 TYR D 653 ARG 0.004 0.000 ARG E 550 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9216 Ramachandran restraints generated. 4608 Oldfield, 0 Emsley, 4608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9216 Ramachandran restraints generated. 4608 Oldfield, 0 Emsley, 4608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 170 time to evaluate : 4.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 HIS cc_start: 0.8361 (OUTLIER) cc_final: 0.7694 (t70) REVERT: A 353 PHE cc_start: 0.6085 (OUTLIER) cc_final: 0.4985 (m-80) REVERT: A 507 GLU cc_start: 0.5952 (OUTLIER) cc_final: 0.5703 (tt0) REVERT: A 626 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7687 (mt) REVERT: A 697 LEU cc_start: 0.7627 (mt) cc_final: 0.7356 (tp) REVERT: B 353 PHE cc_start: 0.6669 (OUTLIER) cc_final: 0.5858 (t80) REVERT: B 584 LEU cc_start: 0.3336 (OUTLIER) cc_final: 0.2600 (pp) REVERT: B 759 ILE cc_start: 0.7067 (OUTLIER) cc_final: 0.6533 (tp) REVERT: C 353 PHE cc_start: 0.6469 (OUTLIER) cc_final: 0.5540 (m-80) REVERT: D 35 MET cc_start: 0.6406 (mtt) cc_final: 0.6165 (mtt) REVERT: D 104 HIS cc_start: 0.8561 (OUTLIER) cc_final: 0.7965 (t70) REVERT: D 353 PHE cc_start: 0.5981 (OUTLIER) cc_final: 0.5183 (t80) REVERT: D 644 LEU cc_start: 0.3307 (OUTLIER) cc_final: 0.2947 (tt) REVERT: E 318 PHE cc_start: 0.8891 (OUTLIER) cc_final: 0.8543 (m-10) REVERT: E 353 PHE cc_start: 0.6066 (OUTLIER) cc_final: 0.4721 (m-80) REVERT: F 35 MET cc_start: 0.6002 (mtt) cc_final: 0.5759 (mtt) REVERT: F 353 PHE cc_start: 0.6397 (OUTLIER) cc_final: 0.5903 (t80) REVERT: F 584 LEU cc_start: 0.3380 (OUTLIER) cc_final: 0.2548 (mt) REVERT: F 605 ARG cc_start: 0.4012 (tpp-160) cc_final: 0.3758 (ptp90) REVERT: F 647 TRP cc_start: 0.6641 (OUTLIER) cc_final: 0.5919 (p90) REVERT: I 45 ARG cc_start: 0.3555 (OUTLIER) cc_final: -0.0100 (mtt180) REVERT: I 68 PHE cc_start: 0.2511 (OUTLIER) cc_final: 0.1547 (m-80) REVERT: I 69 THR cc_start: 0.0989 (OUTLIER) cc_final: 0.0476 (m) REVERT: G 45 ARG cc_start: 0.4246 (OUTLIER) cc_final: 0.1732 (mtt180) REVERT: G 46 GLU cc_start: 0.4114 (tp30) cc_final: 0.2722 (tt0) REVERT: G 68 PHE cc_start: 0.2640 (OUTLIER) cc_final: 0.1775 (m-80) REVERT: G 69 THR cc_start: 0.1260 (OUTLIER) cc_final: 0.0730 (m) REVERT: G 83 MET cc_start: 0.1001 (mpp) cc_final: 0.0520 (mpp) REVERT: H 11 LEU cc_start: 0.2898 (OUTLIER) cc_final: 0.2434 (tt) REVERT: H 45 ARG cc_start: 0.3479 (OUTLIER) cc_final: 0.0410 (mtp85) REVERT: H 68 PHE cc_start: 0.2660 (OUTLIER) cc_final: 0.1972 (m-80) REVERT: H 83 MET cc_start: 0.1240 (mpp) cc_final: 0.0719 (mpp) REVERT: H 102 PHE cc_start: 0.5125 (OUTLIER) cc_final: 0.4750 (t80) outliers start: 151 outliers final: 84 residues processed: 305 average time/residue: 0.4652 time to fit residues: 243.9413 Evaluate side-chains 268 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 158 time to evaluate : 4.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 622 LYS Chi-restraints excluded: chain B residue 637 HIS Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 768 CYS Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 245 GLU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 617 GLN Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 650 HIS Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 318 PHE Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain E residue 527 LEU Chi-restraints excluded: chain E residue 696 ASN Chi-restraints excluded: chain E residue 738 LEU Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 273 ILE Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain F residue 543 LEU Chi-restraints excluded: chain F residue 547 LYS Chi-restraints excluded: chain F residue 584 LEU Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 707 LEU Chi-restraints excluded: chain F residue 736 LEU Chi-restraints excluded: chain I residue 45 ARG Chi-restraints excluded: chain I residue 62 ASP Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 73 ASP Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain G residue 45 ARG Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain G residue 68 PHE Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 45 ARG Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 102 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 412 optimal weight: 10.0000 chunk 313 optimal weight: 7.9990 chunk 216 optimal weight: 0.8980 chunk 46 optimal weight: 8.9990 chunk 199 optimal weight: 10.0000 chunk 280 optimal weight: 0.8980 chunk 419 optimal weight: 0.9980 chunk 443 optimal weight: 5.9990 chunk 218 optimal weight: 9.9990 chunk 397 optimal weight: 1.9990 chunk 119 optimal weight: 6.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN A 650 HIS ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 ASN B 637 HIS ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 GLN ** C 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 624 ASN D 744 GLN E 592 ASN E 660 ASN ** E 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 77 ASN G 77 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 38949 Z= 0.271 Angle : 0.563 10.704 52794 Z= 0.289 Chirality : 0.042 0.153 6081 Planarity : 0.004 0.051 6555 Dihedral : 6.081 59.011 5174 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 4.41 % Allowed : 12.49 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.13), residues: 4608 helix: 0.08 (0.12), residues: 2121 sheet: -0.86 (0.21), residues: 711 loop : -0.47 (0.15), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 647 HIS 0.023 0.001 HIS B 637 PHE 0.024 0.002 PHE I 27 TYR 0.021 0.002 TYR C 281 ARG 0.004 0.000 ARG E 251 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9216 Ramachandran restraints generated. 4608 Oldfield, 0 Emsley, 4608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9216 Ramachandran restraints generated. 4608 Oldfield, 0 Emsley, 4608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 164 time to evaluate : 4.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 HIS cc_start: 0.8657 (OUTLIER) cc_final: 0.7894 (t70) REVERT: A 278 ILE cc_start: 0.8159 (tt) cc_final: 0.7876 (tt) REVERT: A 314 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8516 (mp) REVERT: A 353 PHE cc_start: 0.6325 (OUTLIER) cc_final: 0.4890 (m-80) REVERT: A 507 GLU cc_start: 0.6132 (OUTLIER) cc_final: 0.5893 (tt0) REVERT: A 590 MET cc_start: 0.1910 (mmp) cc_final: 0.1674 (mmp) REVERT: A 647 TRP cc_start: 0.7587 (OUTLIER) cc_final: 0.6923 (p90) REVERT: A 697 LEU cc_start: 0.7715 (mt) cc_final: 0.7427 (tp) REVERT: B 353 PHE cc_start: 0.6709 (OUTLIER) cc_final: 0.6052 (t80) REVERT: B 584 LEU cc_start: 0.3378 (OUTLIER) cc_final: 0.2621 (pp) REVERT: B 759 ILE cc_start: 0.7078 (OUTLIER) cc_final: 0.6534 (tp) REVERT: C 278 ILE cc_start: 0.7921 (OUTLIER) cc_final: 0.7604 (tt) REVERT: C 353 PHE cc_start: 0.6432 (OUTLIER) cc_final: 0.5337 (m-80) REVERT: C 590 MET cc_start: 0.3504 (mmp) cc_final: 0.3030 (mmp) REVERT: C 653 TYR cc_start: 0.4457 (OUTLIER) cc_final: 0.3462 (p90) REVERT: D 104 HIS cc_start: 0.8796 (OUTLIER) cc_final: 0.8478 (t70) REVERT: D 353 PHE cc_start: 0.6012 (OUTLIER) cc_final: 0.5435 (t80) REVERT: D 644 LEU cc_start: 0.2983 (OUTLIER) cc_final: 0.2731 (tt) REVERT: E 314 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8133 (mp) REVERT: E 318 PHE cc_start: 0.8879 (OUTLIER) cc_final: 0.8518 (m-10) REVERT: E 353 PHE cc_start: 0.6105 (OUTLIER) cc_final: 0.4647 (m-80) REVERT: F 353 PHE cc_start: 0.6604 (OUTLIER) cc_final: 0.6211 (t80) REVERT: F 565 VAL cc_start: 0.7738 (OUTLIER) cc_final: 0.7443 (t) REVERT: F 584 LEU cc_start: 0.3101 (OUTLIER) cc_final: 0.2129 (mt) REVERT: F 605 ARG cc_start: 0.4056 (tpp-160) cc_final: 0.3781 (ptp90) REVERT: F 647 TRP cc_start: 0.6770 (OUTLIER) cc_final: 0.5979 (p90) REVERT: I 6 GLU cc_start: 0.3352 (mp0) cc_final: 0.3117 (mp0) REVERT: I 45 ARG cc_start: 0.4076 (OUTLIER) cc_final: 0.0507 (mtt180) REVERT: I 68 PHE cc_start: 0.2653 (OUTLIER) cc_final: 0.1670 (m-80) REVERT: G 45 ARG cc_start: 0.3808 (OUTLIER) cc_final: 0.1483 (ptp-170) REVERT: G 46 GLU cc_start: 0.4387 (tp30) cc_final: 0.3093 (tt0) REVERT: G 68 PHE cc_start: 0.2660 (OUTLIER) cc_final: 0.1870 (m-80) REVERT: G 83 MET cc_start: 0.1069 (mpp) cc_final: 0.0670 (mpp) REVERT: H 11 LEU cc_start: 0.2809 (OUTLIER) cc_final: 0.2434 (tt) REVERT: H 45 ARG cc_start: 0.3579 (OUTLIER) cc_final: 0.0440 (mtp85) REVERT: H 68 PHE cc_start: 0.2782 (OUTLIER) cc_final: 0.2148 (m-80) REVERT: H 83 MET cc_start: 0.1240 (mpp) cc_final: 0.0716 (mpp) REVERT: H 102 PHE cc_start: 0.5107 (OUTLIER) cc_final: 0.4747 (t80) outliers start: 188 outliers final: 125 residues processed: 337 average time/residue: 0.4527 time to fit residues: 263.9349 Evaluate side-chains 306 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 152 time to evaluate : 4.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 647 TRP Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 703 ASP Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 622 LYS Chi-restraints excluded: chain B residue 670 ASN Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 768 CYS Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 653 TYR Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain C residue 800 GLU Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 245 GLU Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 526 ASN Chi-restraints excluded: chain D residue 617 GLN Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 650 HIS Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 771 VAL Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 318 PHE Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain E residue 503 THR Chi-restraints excluded: chain E residue 527 LEU Chi-restraints excluded: chain E residue 696 ASN Chi-restraints excluded: chain E residue 738 LEU Chi-restraints excluded: chain E residue 769 LEU Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 163 CYS Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 273 ILE Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 543 LEU Chi-restraints excluded: chain F residue 547 LYS Chi-restraints excluded: chain F residue 565 VAL Chi-restraints excluded: chain F residue 584 LEU Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 757 THR Chi-restraints excluded: chain F residue 759 ILE Chi-restraints excluded: chain I residue 45 ARG Chi-restraints excluded: chain I residue 62 ASP Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain I residue 73 ASP Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 45 ARG Chi-restraints excluded: chain G residue 68 PHE Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 45 ARG Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 102 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 369 optimal weight: 6.9990 chunk 251 optimal weight: 0.0020 chunk 6 optimal weight: 4.9990 chunk 330 optimal weight: 3.9990 chunk 183 optimal weight: 0.9990 chunk 378 optimal weight: 0.6980 chunk 306 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 226 optimal weight: 0.3980 chunk 398 optimal weight: 8.9990 chunk 111 optimal weight: 8.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 531 ASN ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 GLN ** C 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 522 HIS ** D 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 38949 Z= 0.132 Angle : 0.480 9.316 52794 Z= 0.246 Chirality : 0.040 0.177 6081 Planarity : 0.003 0.052 6555 Dihedral : 5.826 58.866 5172 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.59 % Allowed : 13.92 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.13), residues: 4608 helix: 0.25 (0.12), residues: 2133 sheet: -0.80 (0.21), residues: 699 loop : -0.38 (0.15), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 647 HIS 0.004 0.001 HIS E 132 PHE 0.014 0.001 PHE B 699 TYR 0.016 0.001 TYR D 325 ARG 0.003 0.000 ARG E 550 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9216 Ramachandran restraints generated. 4608 Oldfield, 0 Emsley, 4608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9216 Ramachandran restraints generated. 4608 Oldfield, 0 Emsley, 4608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 161 time to evaluate : 4.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 HIS cc_start: 0.8395 (OUTLIER) cc_final: 0.7709 (t70) REVERT: A 278 ILE cc_start: 0.8215 (tt) cc_final: 0.7946 (tt) REVERT: A 353 PHE cc_start: 0.6092 (OUTLIER) cc_final: 0.5001 (m-80) REVERT: A 626 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7771 (mt) REVERT: A 697 LEU cc_start: 0.7834 (mt) cc_final: 0.7518 (tp) REVERT: B 353 PHE cc_start: 0.6640 (OUTLIER) cc_final: 0.5914 (t80) REVERT: B 584 LEU cc_start: 0.3421 (OUTLIER) cc_final: 0.2820 (pp) REVERT: B 759 ILE cc_start: 0.7087 (OUTLIER) cc_final: 0.6523 (tp) REVERT: C 278 ILE cc_start: 0.7729 (OUTLIER) cc_final: 0.7437 (tt) REVERT: C 353 PHE cc_start: 0.6358 (OUTLIER) cc_final: 0.5273 (m-80) REVERT: C 653 TYR cc_start: 0.4687 (OUTLIER) cc_final: 0.3497 (p90) REVERT: D 35 MET cc_start: 0.6724 (mtt) cc_final: 0.6458 (mtt) REVERT: D 104 HIS cc_start: 0.8612 (OUTLIER) cc_final: 0.7993 (t70) REVERT: D 353 PHE cc_start: 0.5920 (OUTLIER) cc_final: 0.5278 (t80) REVERT: D 644 LEU cc_start: 0.3320 (OUTLIER) cc_final: 0.3027 (tt) REVERT: E 318 PHE cc_start: 0.8889 (OUTLIER) cc_final: 0.8579 (m-10) REVERT: E 353 PHE cc_start: 0.5841 (OUTLIER) cc_final: 0.4590 (m-80) REVERT: F 35 MET cc_start: 0.6001 (mtt) cc_final: 0.5724 (mtt) REVERT: F 353 PHE cc_start: 0.6429 (OUTLIER) cc_final: 0.5988 (t80) REVERT: F 565 VAL cc_start: 0.7716 (OUTLIER) cc_final: 0.7449 (t) REVERT: F 584 LEU cc_start: 0.3573 (OUTLIER) cc_final: 0.2677 (mt) REVERT: F 647 TRP cc_start: 0.6764 (OUTLIER) cc_final: 0.5947 (p90) REVERT: I 6 GLU cc_start: 0.3254 (mp0) cc_final: 0.3041 (mp0) REVERT: I 45 ARG cc_start: 0.3981 (OUTLIER) cc_final: 0.0505 (mtt180) REVERT: I 68 PHE cc_start: 0.2321 (OUTLIER) cc_final: 0.1372 (m-80) REVERT: G 45 ARG cc_start: 0.3467 (OUTLIER) cc_final: 0.1563 (ptp-170) REVERT: G 46 GLU cc_start: 0.4540 (tp30) cc_final: 0.3342 (tt0) REVERT: G 68 PHE cc_start: 0.2223 (OUTLIER) cc_final: 0.1480 (m-80) REVERT: G 83 MET cc_start: 0.1043 (mpp) cc_final: 0.0626 (mpp) REVERT: H 11 LEU cc_start: 0.2883 (OUTLIER) cc_final: 0.2445 (tt) REVERT: H 45 ARG cc_start: 0.3482 (OUTLIER) cc_final: 0.0440 (mtp85) REVERT: H 68 PHE cc_start: 0.2583 (OUTLIER) cc_final: 0.1884 (m-80) REVERT: H 83 MET cc_start: 0.1405 (mpp) cc_final: 0.1074 (mpp) REVERT: H 102 PHE cc_start: 0.5020 (OUTLIER) cc_final: 0.4726 (t80) outliers start: 153 outliers final: 92 residues processed: 297 average time/residue: 0.4563 time to fit residues: 234.5488 Evaluate side-chains 275 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 157 time to evaluate : 4.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 622 LYS Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 768 CYS Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 653 TYR Chi-restraints excluded: chain C residue 800 GLU Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 245 GLU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 508 ILE Chi-restraints excluded: chain D residue 526 ASN Chi-restraints excluded: chain D residue 617 GLN Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 650 HIS Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 771 VAL Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 318 PHE Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain E residue 527 LEU Chi-restraints excluded: chain E residue 696 ASN Chi-restraints excluded: chain E residue 738 LEU Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain F residue 543 LEU Chi-restraints excluded: chain F residue 547 LYS Chi-restraints excluded: chain F residue 565 VAL Chi-restraints excluded: chain F residue 584 LEU Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 654 ILE Chi-restraints excluded: chain F residue 707 LEU Chi-restraints excluded: chain F residue 736 LEU Chi-restraints excluded: chain I residue 45 ARG Chi-restraints excluded: chain I residue 62 ASP Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain I residue 73 ASP Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 45 ARG Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain G residue 68 PHE Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 45 ARG Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 102 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 149 optimal weight: 0.6980 chunk 399 optimal weight: 20.0000 chunk 87 optimal weight: 0.9990 chunk 260 optimal weight: 0.9980 chunk 109 optimal weight: 9.9990 chunk 444 optimal weight: 5.9990 chunk 368 optimal weight: 4.9990 chunk 205 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 146 optimal weight: 4.9990 chunk 233 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 ASN ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 GLN ** C 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 744 GLN ** E 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 709 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 38949 Z= 0.275 Angle : 0.558 8.074 52794 Z= 0.287 Chirality : 0.042 0.157 6081 Planarity : 0.004 0.051 6555 Dihedral : 6.066 59.899 5172 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 4.55 % Allowed : 13.81 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.13), residues: 4608 helix: 0.15 (0.12), residues: 2103 sheet: -0.77 (0.21), residues: 693 loop : -0.47 (0.15), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 647 HIS 0.005 0.001 HIS E 737 PHE 0.020 0.002 PHE C 146 TYR 0.023 0.002 TYR C 281 ARG 0.006 0.000 ARG D 309 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9216 Ramachandran restraints generated. 4608 Oldfield, 0 Emsley, 4608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9216 Ramachandran restraints generated. 4608 Oldfield, 0 Emsley, 4608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 157 time to evaluate : 4.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 HIS cc_start: 0.8670 (OUTLIER) cc_final: 0.7902 (t70) REVERT: A 278 ILE cc_start: 0.8146 (tt) cc_final: 0.7882 (tt) REVERT: A 314 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8511 (mp) REVERT: A 353 PHE cc_start: 0.6221 (OUTLIER) cc_final: 0.4735 (m-80) REVERT: A 507 GLU cc_start: 0.6143 (OUTLIER) cc_final: 0.5895 (tt0) REVERT: A 626 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7865 (mt) REVERT: A 697 LEU cc_start: 0.7710 (mt) cc_final: 0.7439 (tp) REVERT: B 353 PHE cc_start: 0.6713 (OUTLIER) cc_final: 0.6154 (t80) REVERT: B 584 LEU cc_start: 0.3480 (OUTLIER) cc_final: 0.2879 (pp) REVERT: C 278 ILE cc_start: 0.7943 (OUTLIER) cc_final: 0.7603 (tt) REVERT: C 314 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8240 (mp) REVERT: C 353 PHE cc_start: 0.6249 (OUTLIER) cc_final: 0.5026 (m-80) REVERT: C 590 MET cc_start: 0.2476 (mmp) cc_final: 0.2271 (mmm) REVERT: D 35 MET cc_start: 0.6709 (mtt) cc_final: 0.6405 (mtt) REVERT: D 104 HIS cc_start: 0.8807 (OUTLIER) cc_final: 0.8492 (t70) REVERT: D 353 PHE cc_start: 0.6025 (OUTLIER) cc_final: 0.5529 (t80) REVERT: D 434 MET cc_start: 0.5373 (OUTLIER) cc_final: 0.5112 (mtm) REVERT: D 644 LEU cc_start: 0.3356 (OUTLIER) cc_final: 0.3013 (tt) REVERT: E 314 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8122 (mp) REVERT: E 318 PHE cc_start: 0.8882 (OUTLIER) cc_final: 0.8529 (m-10) REVERT: E 353 PHE cc_start: 0.5969 (OUTLIER) cc_final: 0.4299 (m-80) REVERT: E 394 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8001 (mp) REVERT: F 35 MET cc_start: 0.6523 (mtt) cc_final: 0.6287 (mtt) REVERT: F 353 PHE cc_start: 0.6593 (OUTLIER) cc_final: 0.6240 (t80) REVERT: F 565 VAL cc_start: 0.7776 (OUTLIER) cc_final: 0.7447 (t) REVERT: F 584 LEU cc_start: 0.3608 (OUTLIER) cc_final: 0.2679 (mt) REVERT: F 647 TRP cc_start: 0.6792 (OUTLIER) cc_final: 0.5979 (p90) REVERT: I 45 ARG cc_start: 0.3912 (OUTLIER) cc_final: 0.0625 (mtt180) REVERT: I 68 PHE cc_start: 0.2610 (OUTLIER) cc_final: 0.2207 (m-80) REVERT: I 69 THR cc_start: 0.0782 (OUTLIER) cc_final: 0.0191 (m) REVERT: I 83 MET cc_start: 0.0166 (mpp) cc_final: -0.0449 (mpp) REVERT: G 45 ARG cc_start: 0.3657 (OUTLIER) cc_final: 0.1539 (ptp-170) REVERT: G 46 GLU cc_start: 0.4748 (tp30) cc_final: 0.3418 (tt0) REVERT: G 68 PHE cc_start: 0.2462 (OUTLIER) cc_final: 0.1991 (m-80) REVERT: G 83 MET cc_start: 0.1350 (mpp) cc_final: 0.0880 (mpp) REVERT: H 11 LEU cc_start: 0.2986 (OUTLIER) cc_final: 0.2553 (tt) REVERT: H 45 ARG cc_start: 0.3656 (OUTLIER) cc_final: 0.0457 (mtp85) REVERT: H 68 PHE cc_start: 0.2597 (OUTLIER) cc_final: 0.1815 (m-80) REVERT: H 102 PHE cc_start: 0.5047 (OUTLIER) cc_final: 0.4735 (t80) outliers start: 194 outliers final: 132 residues processed: 332 average time/residue: 0.4630 time to fit residues: 270.8512 Evaluate side-chains 312 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 149 time to evaluate : 4.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 703 ASP Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 622 LYS Chi-restraints excluded: chain B residue 670 ASN Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 768 CYS Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 343 MET Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 577 GLU Chi-restraints excluded: chain C residue 715 VAL Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain C residue 800 GLU Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 245 GLU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain D residue 508 ILE Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 526 ASN Chi-restraints excluded: chain D residue 617 GLN Chi-restraints excluded: chain D residue 623 ASP Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 650 HIS Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 265 MET Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 318 PHE Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain E residue 503 THR Chi-restraints excluded: chain E residue 527 LEU Chi-restraints excluded: chain E residue 696 ASN Chi-restraints excluded: chain E residue 738 LEU Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 273 ILE Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain F residue 534 TYR Chi-restraints excluded: chain F residue 543 LEU Chi-restraints excluded: chain F residue 547 LYS Chi-restraints excluded: chain F residue 565 VAL Chi-restraints excluded: chain F residue 584 LEU Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 654 ILE Chi-restraints excluded: chain F residue 663 ASN Chi-restraints excluded: chain F residue 759 ILE Chi-restraints excluded: chain I residue 45 ARG Chi-restraints excluded: chain I residue 62 ASP Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 73 ASP Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 45 ARG Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 68 PHE Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 45 ARG Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 102 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 428 optimal weight: 0.7980 chunk 50 optimal weight: 8.9990 chunk 253 optimal weight: 0.9980 chunk 324 optimal weight: 9.9990 chunk 251 optimal weight: 2.9990 chunk 373 optimal weight: 1.9990 chunk 247 optimal weight: 10.0000 chunk 442 optimal weight: 2.9990 chunk 276 optimal weight: 0.9990 chunk 269 optimal weight: 7.9990 chunk 204 optimal weight: 10.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 696 ASN ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 GLN ** C 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 38949 Z= 0.209 Angle : 0.514 9.024 52794 Z= 0.264 Chirality : 0.041 0.165 6081 Planarity : 0.003 0.047 6555 Dihedral : 6.019 59.479 5172 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 4.22 % Allowed : 14.53 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.13), residues: 4608 helix: 0.19 (0.12), residues: 2103 sheet: -0.79 (0.21), residues: 699 loop : -0.47 (0.15), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 647 HIS 0.004 0.001 HIS F 522 PHE 0.017 0.001 PHE B 699 TYR 0.027 0.001 TYR D 325 ARG 0.003 0.000 ARG E 251 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9216 Ramachandran restraints generated. 4608 Oldfield, 0 Emsley, 4608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9216 Ramachandran restraints generated. 4608 Oldfield, 0 Emsley, 4608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 155 time to evaluate : 4.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 HIS cc_start: 0.8570 (OUTLIER) cc_final: 0.7888 (t70) REVERT: A 278 ILE cc_start: 0.7977 (tt) cc_final: 0.7700 (tt) REVERT: A 353 PHE cc_start: 0.6084 (OUTLIER) cc_final: 0.4719 (m-80) REVERT: A 394 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8127 (mp) REVERT: A 507 GLU cc_start: 0.6127 (OUTLIER) cc_final: 0.5356 (tt0) REVERT: A 626 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7807 (mt) REVERT: A 697 LEU cc_start: 0.7884 (mt) cc_final: 0.7497 (tp) REVERT: B 353 PHE cc_start: 0.6726 (OUTLIER) cc_final: 0.6133 (t80) REVERT: B 584 LEU cc_start: 0.3265 (OUTLIER) cc_final: 0.2798 (pp) REVERT: C 278 ILE cc_start: 0.7869 (OUTLIER) cc_final: 0.7563 (tt) REVERT: C 314 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8231 (mp) REVERT: C 353 PHE cc_start: 0.6175 (OUTLIER) cc_final: 0.4969 (m-80) REVERT: C 590 MET cc_start: 0.3946 (mmp) cc_final: 0.3570 (mmm) REVERT: D 35 MET cc_start: 0.6324 (mtt) cc_final: 0.6038 (mtt) REVERT: D 104 HIS cc_start: 0.8756 (OUTLIER) cc_final: 0.8330 (t70) REVERT: D 353 PHE cc_start: 0.6073 (OUTLIER) cc_final: 0.5530 (t80) REVERT: D 590 MET cc_start: 0.4847 (mtt) cc_final: 0.4630 (mtt) REVERT: D 644 LEU cc_start: 0.3330 (OUTLIER) cc_final: 0.2989 (tt) REVERT: E 318 PHE cc_start: 0.8906 (OUTLIER) cc_final: 0.8562 (m-10) REVERT: E 353 PHE cc_start: 0.5666 (OUTLIER) cc_final: 0.4227 (m-80) REVERT: E 394 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8051 (mp) REVERT: F 35 MET cc_start: 0.6494 (mtt) cc_final: 0.6233 (mtt) REVERT: F 353 PHE cc_start: 0.6554 (OUTLIER) cc_final: 0.6193 (t80) REVERT: F 565 VAL cc_start: 0.7403 (OUTLIER) cc_final: 0.7167 (t) REVERT: F 584 LEU cc_start: 0.3604 (OUTLIER) cc_final: 0.2810 (mt) REVERT: F 647 TRP cc_start: 0.6809 (OUTLIER) cc_final: 0.5988 (p90) REVERT: I 45 ARG cc_start: 0.3906 (OUTLIER) cc_final: 0.0636 (mtt180) REVERT: I 68 PHE cc_start: 0.2587 (OUTLIER) cc_final: 0.2158 (m-80) REVERT: I 83 MET cc_start: 0.0356 (mpp) cc_final: -0.0252 (mpp) REVERT: G 27 PHE cc_start: 0.5535 (t80) cc_final: 0.5246 (t80) REVERT: G 45 ARG cc_start: 0.3835 (OUTLIER) cc_final: 0.1580 (ptp-170) REVERT: G 46 GLU cc_start: 0.5094 (tp30) cc_final: 0.3855 (tt0) REVERT: G 68 PHE cc_start: 0.2536 (OUTLIER) cc_final: 0.1978 (m-80) REVERT: G 83 MET cc_start: 0.1287 (mpp) cc_final: 0.0860 (mpp) REVERT: H 11 LEU cc_start: 0.3055 (OUTLIER) cc_final: 0.2616 (tt) REVERT: H 45 ARG cc_start: 0.3668 (OUTLIER) cc_final: 0.0475 (mtp85) REVERT: H 68 PHE cc_start: 0.2906 (OUTLIER) cc_final: 0.2068 (m-80) REVERT: H 102 PHE cc_start: 0.4959 (OUTLIER) cc_final: 0.4670 (t80) outliers start: 180 outliers final: 126 residues processed: 319 average time/residue: 0.4573 time to fit residues: 254.1772 Evaluate side-chains 305 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 151 time to evaluate : 4.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 703 ASP Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 622 LYS Chi-restraints excluded: chain B residue 670 ASN Chi-restraints excluded: chain B residue 696 ASN Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 768 CYS Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 343 MET Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 577 GLU Chi-restraints excluded: chain C residue 800 GLU Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 163 CYS Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 245 GLU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 508 ILE Chi-restraints excluded: chain D residue 526 ASN Chi-restraints excluded: chain D residue 570 GLN Chi-restraints excluded: chain D residue 617 GLN Chi-restraints excluded: chain D residue 623 ASP Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 650 HIS Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 318 PHE Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain E residue 503 THR Chi-restraints excluded: chain E residue 527 LEU Chi-restraints excluded: chain E residue 696 ASN Chi-restraints excluded: chain E residue 738 LEU Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain F residue 543 LEU Chi-restraints excluded: chain F residue 565 VAL Chi-restraints excluded: chain F residue 584 LEU Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 654 ILE Chi-restraints excluded: chain F residue 663 ASN Chi-restraints excluded: chain F residue 707 LEU Chi-restraints excluded: chain F residue 759 ILE Chi-restraints excluded: chain I residue 45 ARG Chi-restraints excluded: chain I residue 62 ASP Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain I residue 73 ASP Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 45 ARG Chi-restraints excluded: chain G residue 68 PHE Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 45 ARG Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 102 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 273 optimal weight: 5.9990 chunk 176 optimal weight: 5.9990 chunk 264 optimal weight: 6.9990 chunk 133 optimal weight: 10.0000 chunk 86 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 281 optimal weight: 0.0980 chunk 301 optimal weight: 0.9980 chunk 218 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 347 optimal weight: 0.0980 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 531 ASN ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 GLN C 478 HIS ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 615 ASN ** D 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 38949 Z= 0.239 Angle : 0.535 8.389 52794 Z= 0.275 Chirality : 0.041 0.161 6081 Planarity : 0.003 0.044 6555 Dihedral : 6.056 59.852 5172 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 4.50 % Allowed : 14.51 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.13), residues: 4608 helix: 0.13 (0.12), residues: 2103 sheet: -0.78 (0.21), residues: 699 loop : -0.52 (0.15), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 647 HIS 0.004 0.001 HIS B 694 PHE 0.019 0.001 PHE A 250 TYR 0.027 0.001 TYR D 325 ARG 0.004 0.000 ARG E 762 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9216 Ramachandran restraints generated. 4608 Oldfield, 0 Emsley, 4608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9216 Ramachandran restraints generated. 4608 Oldfield, 0 Emsley, 4608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 152 time to evaluate : 4.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 HIS cc_start: 0.8610 (OUTLIER) cc_final: 0.7920 (t70) REVERT: A 278 ILE cc_start: 0.7987 (tt) cc_final: 0.7731 (tt) REVERT: A 353 PHE cc_start: 0.6129 (OUTLIER) cc_final: 0.4686 (m-80) REVERT: A 394 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8139 (mp) REVERT: A 507 GLU cc_start: 0.6080 (OUTLIER) cc_final: 0.5798 (tt0) REVERT: A 626 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7837 (mt) REVERT: A 647 TRP cc_start: 0.7574 (OUTLIER) cc_final: 0.6917 (p90) REVERT: A 697 LEU cc_start: 0.7874 (mt) cc_final: 0.7491 (tp) REVERT: B 353 PHE cc_start: 0.6760 (OUTLIER) cc_final: 0.6156 (t80) REVERT: B 584 LEU cc_start: 0.3142 (OUTLIER) cc_final: 0.2693 (pp) REVERT: B 696 ASN cc_start: 0.4588 (OUTLIER) cc_final: 0.3555 (p0) REVERT: C 278 ILE cc_start: 0.7888 (OUTLIER) cc_final: 0.7574 (tt) REVERT: C 314 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8247 (mp) REVERT: C 353 PHE cc_start: 0.6192 (OUTLIER) cc_final: 0.4964 (m-80) REVERT: C 590 MET cc_start: 0.4010 (mmp) cc_final: 0.3654 (mmm) REVERT: D 35 MET cc_start: 0.6428 (mtt) cc_final: 0.6115 (mtt) REVERT: D 104 HIS cc_start: 0.8791 (OUTLIER) cc_final: 0.8400 (t70) REVERT: D 353 PHE cc_start: 0.6086 (OUTLIER) cc_final: 0.5616 (t80) REVERT: D 590 MET cc_start: 0.4880 (mtt) cc_final: 0.4666 (mtt) REVERT: D 644 LEU cc_start: 0.3508 (OUTLIER) cc_final: 0.3198 (tt) REVERT: E 314 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8091 (mp) REVERT: E 318 PHE cc_start: 0.8902 (OUTLIER) cc_final: 0.8532 (m-10) REVERT: E 353 PHE cc_start: 0.5941 (OUTLIER) cc_final: 0.4374 (m-80) REVERT: E 394 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8048 (mp) REVERT: F 35 MET cc_start: 0.6519 (mtt) cc_final: 0.6249 (mtt) REVERT: F 353 PHE cc_start: 0.6584 (OUTLIER) cc_final: 0.6212 (t80) REVERT: F 584 LEU cc_start: 0.3613 (OUTLIER) cc_final: 0.2681 (mt) REVERT: F 647 TRP cc_start: 0.6824 (OUTLIER) cc_final: 0.6004 (p90) REVERT: I 45 ARG cc_start: 0.4112 (OUTLIER) cc_final: 0.0816 (mtt180) REVERT: I 68 PHE cc_start: 0.2393 (OUTLIER) cc_final: 0.2025 (m-80) REVERT: I 83 MET cc_start: 0.0402 (mpp) cc_final: -0.0221 (mpp) REVERT: G 27 PHE cc_start: 0.5707 (t80) cc_final: 0.5444 (t80) REVERT: G 45 ARG cc_start: 0.3970 (OUTLIER) cc_final: 0.1676 (ptp-170) REVERT: G 46 GLU cc_start: 0.5128 (tp30) cc_final: 0.3871 (tt0) REVERT: G 68 PHE cc_start: 0.2573 (OUTLIER) cc_final: 0.2024 (m-80) REVERT: G 83 MET cc_start: 0.1335 (mpp) cc_final: 0.0902 (mpp) REVERT: H 11 LEU cc_start: 0.3068 (OUTLIER) cc_final: 0.2702 (tt) REVERT: H 45 ARG cc_start: 0.3847 (OUTLIER) cc_final: 0.0643 (mtp85) REVERT: H 68 PHE cc_start: 0.2828 (OUTLIER) cc_final: 0.2064 (m-80) REVERT: H 102 PHE cc_start: 0.5098 (OUTLIER) cc_final: 0.4823 (t80) outliers start: 192 outliers final: 142 residues processed: 330 average time/residue: 0.4437 time to fit residues: 254.2584 Evaluate side-chains 321 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 149 time to evaluate : 4.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 647 TRP Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 703 ASP Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 786 VAL Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 622 LYS Chi-restraints excluded: chain B residue 670 ASN Chi-restraints excluded: chain B residue 696 ASN Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 768 CYS Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 343 MET Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 577 GLU Chi-restraints excluded: chain C residue 715 VAL Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain C residue 800 GLU Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 163 CYS Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 245 GLU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 508 ILE Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 526 ASN Chi-restraints excluded: chain D residue 570 GLN Chi-restraints excluded: chain D residue 617 GLN Chi-restraints excluded: chain D residue 623 ASP Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 650 HIS Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 265 MET Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 318 PHE Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain E residue 503 THR Chi-restraints excluded: chain E residue 527 LEU Chi-restraints excluded: chain E residue 696 ASN Chi-restraints excluded: chain E residue 738 LEU Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain F residue 534 TYR Chi-restraints excluded: chain F residue 543 LEU Chi-restraints excluded: chain F residue 584 LEU Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 654 ILE Chi-restraints excluded: chain F residue 663 ASN Chi-restraints excluded: chain F residue 707 LEU Chi-restraints excluded: chain F residue 736 LEU Chi-restraints excluded: chain F residue 759 ILE Chi-restraints excluded: chain I residue 45 ARG Chi-restraints excluded: chain I residue 62 ASP Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain I residue 73 ASP Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 45 ARG Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 68 PHE Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 45 ARG Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 102 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 402 optimal weight: 1.9990 chunk 423 optimal weight: 4.9990 chunk 386 optimal weight: 3.9990 chunk 412 optimal weight: 7.9990 chunk 248 optimal weight: 4.9990 chunk 179 optimal weight: 9.9990 chunk 323 optimal weight: 0.9980 chunk 126 optimal weight: 10.0000 chunk 372 optimal weight: 0.7980 chunk 389 optimal weight: 7.9990 chunk 410 optimal weight: 5.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 ASN B 696 ASN ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 554 ASN ** D 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 744 GLN ** E 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 744 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 38949 Z= 0.322 Angle : 0.603 9.132 52794 Z= 0.310 Chirality : 0.043 0.169 6081 Planarity : 0.004 0.045 6555 Dihedral : 6.333 58.682 5172 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 17.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 4.55 % Allowed : 15.05 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.13), residues: 4608 helix: -0.03 (0.12), residues: 2082 sheet: -0.87 (0.21), residues: 699 loop : -0.72 (0.15), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 647 HIS 0.006 0.001 HIS F 522 PHE 0.023 0.002 PHE B 699 TYR 0.025 0.002 TYR E 281 ARG 0.004 0.001 ARG E 251 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9216 Ramachandran restraints generated. 4608 Oldfield, 0 Emsley, 4608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9216 Ramachandran restraints generated. 4608 Oldfield, 0 Emsley, 4608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 152 time to evaluate : 4.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 HIS cc_start: 0.8752 (OUTLIER) cc_final: 0.8021 (t70) REVERT: A 314 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8536 (mp) REVERT: A 353 PHE cc_start: 0.6180 (OUTLIER) cc_final: 0.4626 (m-80) REVERT: A 394 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8237 (mp) REVERT: A 507 GLU cc_start: 0.6111 (OUTLIER) cc_final: 0.5803 (tt0) REVERT: A 590 MET cc_start: 0.3869 (mmp) cc_final: 0.3391 (mmp) REVERT: A 626 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7783 (mt) REVERT: A 647 TRP cc_start: 0.7600 (OUTLIER) cc_final: 0.7100 (p90) REVERT: A 697 LEU cc_start: 0.8027 (mt) cc_final: 0.7621 (tp) REVERT: B 353 PHE cc_start: 0.6944 (OUTLIER) cc_final: 0.6472 (t80) REVERT: B 584 LEU cc_start: 0.3088 (OUTLIER) cc_final: 0.2681 (pp) REVERT: B 619 ILE cc_start: 0.4505 (OUTLIER) cc_final: 0.4305 (tp) REVERT: B 696 ASN cc_start: 0.4890 (OUTLIER) cc_final: 0.3877 (p0) REVERT: C 278 ILE cc_start: 0.7988 (OUTLIER) cc_final: 0.7651 (tt) REVERT: C 314 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8269 (mp) REVERT: C 353 PHE cc_start: 0.6243 (OUTLIER) cc_final: 0.4902 (m-80) REVERT: D 35 MET cc_start: 0.6754 (mtt) cc_final: 0.6514 (mtt) REVERT: D 104 HIS cc_start: 0.8817 (OUTLIER) cc_final: 0.8564 (t70) REVERT: D 353 PHE cc_start: 0.6130 (OUTLIER) cc_final: 0.5712 (t80) REVERT: D 644 LEU cc_start: 0.3374 (OUTLIER) cc_final: 0.3143 (tt) REVERT: D 775 GLU cc_start: 0.3313 (OUTLIER) cc_final: 0.2921 (mm-30) REVERT: E 314 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8102 (mp) REVERT: E 318 PHE cc_start: 0.8921 (OUTLIER) cc_final: 0.8531 (m-10) REVERT: E 353 PHE cc_start: 0.5855 (OUTLIER) cc_final: 0.4276 (m-80) REVERT: E 394 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8079 (mp) REVERT: F 353 PHE cc_start: 0.6752 (OUTLIER) cc_final: 0.6489 (t80) REVERT: F 584 LEU cc_start: 0.3327 (OUTLIER) cc_final: 0.2399 (mt) REVERT: F 647 TRP cc_start: 0.6944 (OUTLIER) cc_final: 0.6063 (p90) REVERT: I 45 ARG cc_start: 0.4429 (OUTLIER) cc_final: 0.1091 (mtt180) REVERT: I 68 PHE cc_start: 0.2132 (OUTLIER) cc_final: 0.1607 (m-80) REVERT: G 45 ARG cc_start: 0.4213 (OUTLIER) cc_final: 0.1647 (ptp-170) REVERT: G 46 GLU cc_start: 0.5412 (tp30) cc_final: 0.4146 (tt0) REVERT: G 68 PHE cc_start: 0.2768 (OUTLIER) cc_final: 0.2277 (m-80) REVERT: G 83 MET cc_start: 0.1426 (mpp) cc_final: 0.0987 (mpp) REVERT: H 11 LEU cc_start: 0.2964 (OUTLIER) cc_final: 0.2644 (tt) REVERT: H 45 ARG cc_start: 0.3868 (OUTLIER) cc_final: 0.0826 (mtt180) REVERT: H 68 PHE cc_start: 0.2841 (OUTLIER) cc_final: 0.2173 (m-80) REVERT: H 102 PHE cc_start: 0.5120 (OUTLIER) cc_final: 0.4818 (t80) outliers start: 194 outliers final: 143 residues processed: 333 average time/residue: 0.4606 time to fit residues: 266.4017 Evaluate side-chains 315 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 139 time to evaluate : 4.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 647 TRP Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 703 ASP Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 786 VAL Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 622 LYS Chi-restraints excluded: chain B residue 670 ASN Chi-restraints excluded: chain B residue 696 ASN Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 768 CYS Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 343 MET Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 577 GLU Chi-restraints excluded: chain C residue 715 VAL Chi-restraints excluded: chain C residue 743 LEU Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain C residue 800 GLU Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 163 CYS Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 245 GLU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 508 ILE Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 570 GLN Chi-restraints excluded: chain D residue 617 GLN Chi-restraints excluded: chain D residue 623 ASP Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 775 GLU Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 265 MET Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 318 PHE Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain E residue 503 THR Chi-restraints excluded: chain E residue 527 LEU Chi-restraints excluded: chain E residue 696 ASN Chi-restraints excluded: chain E residue 738 LEU Chi-restraints excluded: chain E residue 769 LEU Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 273 ILE Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain F residue 527 LEU Chi-restraints excluded: chain F residue 534 TYR Chi-restraints excluded: chain F residue 543 LEU Chi-restraints excluded: chain F residue 584 LEU Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 654 ILE Chi-restraints excluded: chain F residue 663 ASN Chi-restraints excluded: chain F residue 759 ILE Chi-restraints excluded: chain I residue 45 ARG Chi-restraints excluded: chain I residue 62 ASP Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain I residue 73 ASP Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 45 ARG Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 68 PHE Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 45 ARG Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 102 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 270 optimal weight: 10.0000 chunk 435 optimal weight: 2.9990 chunk 266 optimal weight: 3.9990 chunk 206 optimal weight: 10.0000 chunk 303 optimal weight: 0.8980 chunk 457 optimal weight: 9.9990 chunk 420 optimal weight: 0.9980 chunk 364 optimal weight: 0.6980 chunk 37 optimal weight: 5.9990 chunk 281 optimal weight: 5.9990 chunk 223 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 ASN B 696 ASN ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 GLN D 554 ASN ** D 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 38949 Z= 0.232 Angle : 0.545 8.508 52794 Z= 0.279 Chirality : 0.042 0.152 6081 Planarity : 0.003 0.043 6555 Dihedral : 6.188 58.844 5172 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 4.15 % Allowed : 15.45 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.13), residues: 4608 helix: 0.05 (0.12), residues: 2079 sheet: -0.80 (0.21), residues: 729 loop : -0.64 (0.15), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 647 HIS 0.005 0.001 HIS B 694 PHE 0.018 0.001 PHE E 146 TYR 0.031 0.002 TYR D 325 ARG 0.008 0.000 ARG D 357 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9216 Ramachandran restraints generated. 4608 Oldfield, 0 Emsley, 4608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9216 Ramachandran restraints generated. 4608 Oldfield, 0 Emsley, 4608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 149 time to evaluate : 4.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 HIS cc_start: 0.8658 (OUTLIER) cc_final: 0.7959 (t70) REVERT: A 278 ILE cc_start: 0.8119 (tt) cc_final: 0.7860 (tt) REVERT: A 314 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8479 (mp) REVERT: A 353 PHE cc_start: 0.6187 (OUTLIER) cc_final: 0.4784 (m-80) REVERT: A 394 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8222 (mp) REVERT: A 507 GLU cc_start: 0.6121 (OUTLIER) cc_final: 0.5485 (tt0) REVERT: A 590 MET cc_start: 0.3870 (mmp) cc_final: 0.3577 (mmp) REVERT: A 626 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7790 (mt) REVERT: A 647 TRP cc_start: 0.7589 (OUTLIER) cc_final: 0.7030 (p90) REVERT: A 697 LEU cc_start: 0.8086 (mt) cc_final: 0.7698 (tp) REVERT: B 353 PHE cc_start: 0.6905 (OUTLIER) cc_final: 0.6420 (t80) REVERT: B 584 LEU cc_start: 0.2992 (OUTLIER) cc_final: 0.2610 (pp) REVERT: C 278 ILE cc_start: 0.7922 (OUTLIER) cc_final: 0.7607 (tt) REVERT: C 314 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8197 (mp) REVERT: C 353 PHE cc_start: 0.6379 (OUTLIER) cc_final: 0.5083 (m-80) REVERT: D 35 MET cc_start: 0.6424 (mtt) cc_final: 0.6105 (mtt) REVERT: D 104 HIS cc_start: 0.8787 (OUTLIER) cc_final: 0.8437 (t70) REVERT: D 353 PHE cc_start: 0.6155 (OUTLIER) cc_final: 0.5819 (t80) REVERT: D 644 LEU cc_start: 0.3270 (OUTLIER) cc_final: 0.2979 (tt) REVERT: D 775 GLU cc_start: 0.3298 (OUTLIER) cc_final: 0.2919 (mm-30) REVERT: E 314 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8072 (mp) REVERT: E 318 PHE cc_start: 0.8891 (OUTLIER) cc_final: 0.8521 (m-10) REVERT: E 353 PHE cc_start: 0.5791 (OUTLIER) cc_final: 0.4287 (m-80) REVERT: E 394 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8079 (mp) REVERT: F 35 MET cc_start: 0.6664 (mtt) cc_final: 0.6343 (mtt) REVERT: F 353 PHE cc_start: 0.6646 (OUTLIER) cc_final: 0.6368 (t80) REVERT: F 584 LEU cc_start: 0.3342 (OUTLIER) cc_final: 0.2420 (mt) REVERT: F 647 TRP cc_start: 0.6952 (OUTLIER) cc_final: 0.6068 (p90) REVERT: I 45 ARG cc_start: 0.4492 (OUTLIER) cc_final: 0.1082 (mtt180) REVERT: I 68 PHE cc_start: 0.2221 (OUTLIER) cc_final: 0.1896 (m-80) REVERT: I 83 MET cc_start: 0.0587 (mpp) cc_final: 0.0115 (tpp) REVERT: G 45 ARG cc_start: 0.4126 (OUTLIER) cc_final: 0.1626 (ptp-170) REVERT: G 46 GLU cc_start: 0.5422 (tp30) cc_final: 0.4152 (tt0) REVERT: G 68 PHE cc_start: 0.2618 (OUTLIER) cc_final: 0.2162 (m-80) REVERT: G 83 MET cc_start: 0.1409 (mpp) cc_final: 0.0984 (mpp) REVERT: H 11 LEU cc_start: 0.3094 (OUTLIER) cc_final: 0.2727 (tt) REVERT: H 45 ARG cc_start: 0.4080 (OUTLIER) cc_final: 0.1044 (mtt180) REVERT: H 68 PHE cc_start: 0.2862 (OUTLIER) cc_final: 0.2289 (m-80) REVERT: H 102 PHE cc_start: 0.5077 (OUTLIER) cc_final: 0.4778 (t80) outliers start: 177 outliers final: 139 residues processed: 316 average time/residue: 0.4919 time to fit residues: 272.8733 Evaluate side-chains 315 residues out of total 4266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 145 time to evaluate : 4.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 647 TRP Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 703 ASP Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 786 VAL Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 622 LYS Chi-restraints excluded: chain B residue 670 ASN Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 768 CYS Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 343 MET Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 577 GLU Chi-restraints excluded: chain C residue 715 VAL Chi-restraints excluded: chain C residue 743 LEU Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain C residue 800 GLU Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 163 CYS Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 245 GLU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 508 ILE Chi-restraints excluded: chain D residue 570 GLN Chi-restraints excluded: chain D residue 617 GLN Chi-restraints excluded: chain D residue 623 ASP Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 715 VAL Chi-restraints excluded: chain D residue 775 GLU Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 265 MET Chi-restraints excluded: chain E residue 267 GLN Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 318 PHE Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain E residue 503 THR Chi-restraints excluded: chain E residue 527 LEU Chi-restraints excluded: chain E residue 696 ASN Chi-restraints excluded: chain E residue 738 LEU Chi-restraints excluded: chain E residue 769 LEU Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 273 ILE Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain F residue 527 LEU Chi-restraints excluded: chain F residue 534 TYR Chi-restraints excluded: chain F residue 543 LEU Chi-restraints excluded: chain F residue 584 LEU Chi-restraints excluded: chain F residue 591 VAL Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 654 ILE Chi-restraints excluded: chain F residue 663 ASN Chi-restraints excluded: chain F residue 759 ILE Chi-restraints excluded: chain I residue 45 ARG Chi-restraints excluded: chain I residue 62 ASP Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain I residue 73 ASP Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 45 ARG Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 68 PHE Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 45 ARG Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 102 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 289 optimal weight: 0.9980 chunk 387 optimal weight: 10.0000 chunk 111 optimal weight: 3.9990 chunk 335 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 101 optimal weight: 0.9990 chunk 364 optimal weight: 0.9990 chunk 152 optimal weight: 1.9990 chunk 374 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 67 optimal weight: 9.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 617 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.109999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.094766 restraints weight = 122680.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.094379 restraints weight = 172929.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.094808 restraints weight = 147103.192| |-----------------------------------------------------------------------------| r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6683 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 38949 Z= 0.183 Angle : 0.521 10.194 52794 Z= 0.266 Chirality : 0.041 0.304 6081 Planarity : 0.003 0.043 6555 Dihedral : 6.054 59.359 5172 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 3.94 % Allowed : 15.85 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.13), residues: 4608 helix: 0.22 (0.12), residues: 2061 sheet: -0.69 (0.21), residues: 723 loop : -0.59 (0.15), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 647 HIS 0.004 0.001 HIS E 132 PHE 0.038 0.001 PHE B 699 TYR 0.027 0.001 TYR D 325 ARG 0.009 0.000 ARG D 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6406.24 seconds wall clock time: 120 minutes 6.88 seconds (7206.88 seconds total)