Starting phenix.real_space_refine (version: 1.21rc1) on Mon Jul 17 15:33:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p60_13213/07_2023/7p60_13213.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p60_13213/07_2023/7p60_13213.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/7p60_13213/07_2023/7p60_13213.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p60_13213/07_2023/7p60_13213.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p60_13213/07_2023/7p60_13213.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p60_13213/07_2023/7p60_13213.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 159 5.16 5 C 24939 2.51 5 N 6450 2.21 5 O 6858 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 165": "OD1" <-> "OD2" Residue "B ASP 233": "OD1" <-> "OD2" Residue "B PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 165": "OD1" <-> "OD2" Residue "D PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 281": "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 GLU 358": "OE1" <-> "OE2" Residue "E PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 691": "OD1" <-> "OD2" Residue "G TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 38406 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: "G" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 958 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "I" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 958 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "H" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 958 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Time building chain proxies: 17.20, per 1000 atoms: 0.45 Number of scatterers: 38406 At special positions: 0 Unit cell: (156.24, 153.636, 192.696, 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 159 16.00 O 6858 8.00 N 6450 7.00 C 24939 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 G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 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: 14.66 Conformation dependent library (CDL) restraints added in 5.2 seconds 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9006 Finding SS restraints... Secondary structure from input PDB file: 195 helices and 29 sheets defined 49.0% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.60 Creating SS restraints... Processing helix chain 'A' and resid 16 through 21 removed outlier: 3.679A pdb=" N ILE A 19 " --> pdb=" O ALA A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 49 Processing helix chain 'A' and resid 102 through 117 Processing helix chain 'A' and resid 119 through 146 Proline residue: A 126 - end of helix removed outlier: 4.925A pdb=" N TRP A 143 " --> pdb=" O CYS A 139 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N PHE A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 165 removed outlier: 3.652A pdb=" N LYS A 152 " --> pdb=" O ARG A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 176 removed outlier: 3.665A pdb=" N THR A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR A 176 " --> pdb=" O ALA A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 255 removed outlier: 3.526A 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 299 through 304 removed outlier: 3.815A pdb=" N THR A 303 " --> pdb=" O ILE A 299 " (cutoff:3.500A) 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: 4.395A pdb=" N SER A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 411 Processing helix chain 'A' and resid 412 through 420 Processing helix chain 'A' and resid 439 through 445 removed outlier: 3.786A pdb=" N LEU A 445 " --> pdb=" O VAL A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 468 Processing helix chain 'A' and resid 484 through 492 Processing helix chain 'A' and resid 509 through 515 removed outlier: 3.753A pdb=" N ILE A 512 " --> pdb=" O PRO A 509 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TYR A 513 " --> pdb=" O LEU A 510 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A 515 " --> pdb=" O ILE A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 543 removed outlier: 4.098A 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 608 through 613 Processing helix chain 'A' and resid 629 through 637 Processing helix chain 'A' and resid 655 through 661 removed outlier: 3.561A pdb=" N ILE A 658 " --> pdb=" O PRO A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 684 Processing helix chain 'A' and resid 701 through 707 Processing helix chain 'A' and resid 724 through 730 Processing helix chain 'A' and resid 747 through 753 Processing helix chain 'A' and resid 771 through 776 removed outlier: 3.695A 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: 3.676A pdb=" N GLU A 808 " --> pdb=" O ARG A 804 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 21 removed outlier: 4.041A 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 146 Proline residue: B 126 - end of helix removed outlier: 4.940A pdb=" N TRP B 143 " --> pdb=" O CYS B 139 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N PHE B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 166 removed outlier: 4.020A pdb=" N LYS B 152 " --> pdb=" O ARG B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 176 removed outlier: 4.068A pdb=" N THR B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 256 removed outlier: 4.144A pdb=" N GLU B 256 " --> pdb=" O THR B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 287 removed outlier: 4.624A pdb=" N HIS B 287 " --> pdb=" O VAL B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 344 Processing helix chain 'B' and resid 353 through 360 Processing helix chain 'B' and resid 372 through 383 Processing helix chain 'B' and resid 383 through 392 removed outlier: 4.120A pdb=" N SER B 387 " --> pdb=" O ASP B 383 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL B 392 " --> pdb=" O LYS B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 411 Processing helix chain 'B' and resid 412 through 420 Processing helix chain 'B' and resid 439 through 445 removed outlier: 3.615A pdb=" N PHE B 443 " --> pdb=" O ASP B 440 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASP B 444 " --> pdb=" O THR B 441 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU B 445 " --> pdb=" O VAL B 442 " (cutoff:3.500A) 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: 3.818A pdb=" N TYR B 513 " --> pdb=" O LEU B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 543 removed outlier: 3.613A pdb=" N GLY B 539 " --> pdb=" O VAL B 536 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG B 541 " --> pdb=" O ASP B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 566 Processing helix chain 'B' and resid 607 through 611 removed outlier: 3.528A pdb=" N ILE B 610 " --> pdb=" O PRO B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 638 removed outlier: 3.729A pdb=" N GLN B 636 " --> pdb=" O ILE B 633 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N HIS B 637 " --> pdb=" O SER B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 660 removed outlier: 3.640A pdb=" N ILE B 658 " --> pdb=" O PRO B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 684 removed outlier: 3.700A pdb=" N CYS B 684 " --> pdb=" O LEU B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 707 removed outlier: 3.750A pdb=" N GLY B 705 " --> pdb=" O ALA B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 730 removed outlier: 3.655A pdb=" N CYS B 730 " --> pdb=" O LEU B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 753 removed outlier: 3.686A pdb=" N VAL B 750 " --> pdb=" O PRO B 747 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLY B 751 " --> pdb=" O SER B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 776 removed outlier: 3.613A 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: 3.583A pdb=" N ILE C 19 " --> pdb=" O ALA C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 49 Processing helix chain 'C' and resid 102 through 117 Processing helix chain 'C' and resid 119 through 146 Proline residue: C 126 - end of helix removed outlier: 4.829A pdb=" N TRP C 143 " --> pdb=" O CYS C 139 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N PHE C 144 " --> pdb=" O SER C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 165 removed outlier: 3.882A pdb=" N LYS C 152 " --> pdb=" O ARG C 148 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP C 165 " --> pdb=" O LEU C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 176 removed outlier: 3.661A pdb=" N THR C 170 " --> pdb=" O SER C 166 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR C 176 " --> pdb=" O ALA C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 255 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 299 through 304 removed outlier: 3.824A pdb=" N THR C 303 " --> pdb=" O ILE C 299 " (cutoff:3.500A) 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: 4.332A pdb=" N SER C 387 " --> pdb=" O ASP C 383 " (cutoff:3.500A) removed outlier: 3.699A 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 420 Processing helix chain 'C' and resid 439 through 445 removed outlier: 3.568A pdb=" N VAL C 442 " --> pdb=" O PRO C 439 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE C 443 " --> pdb=" O ASP C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 484 through 492 Processing helix chain 'C' and resid 504 through 508 Processing helix chain 'C' and resid 509 through 515 removed outlier: 3.816A pdb=" N ILE C 512 " --> pdb=" O PRO C 509 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N TYR C 513 " --> pdb=" O LEU C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 543 removed outlier: 4.128A pdb=" N ARG C 541 " --> pdb=" O ASP C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 566 Processing helix chain 'C' and resid 607 through 613 removed outlier: 3.981A pdb=" N ILE C 610 " --> pdb=" O PRO C 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 638 removed outlier: 3.501A pdb=" N GLN C 636 " --> pdb=" O ILE C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 661 removed outlier: 3.777A pdb=" N ILE C 658 " --> pdb=" O PRO C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 678 through 684 Processing helix chain 'C' and resid 701 through 707 removed outlier: 3.598A pdb=" N ILE C 704 " --> pdb=" O PRO C 701 " (cutoff:3.500A) Processing helix chain 'C' and resid 724 through 730 Processing helix chain 'C' and resid 747 through 753 removed outlier: 3.564A pdb=" N VAL C 750 " --> pdb=" O PRO C 747 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY C 751 " --> pdb=" O SER C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 770 through 776 removed outlier: 3.592A pdb=" N LEU C 773 " --> pdb=" O PRO C 770 " (cutoff:3.500A) removed outlier: 3.933A 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 removed outlier: 3.679A pdb=" N GLU C 808 " --> pdb=" O ARG C 804 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 21 removed outlier: 3.704A 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 146 Proline residue: D 126 - end of helix removed outlier: 4.957A pdb=" N TRP D 143 " --> pdb=" O CYS D 139 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N PHE D 144 " --> pdb=" O SER D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 166 removed outlier: 4.154A pdb=" N LYS D 152 " --> pdb=" O ARG D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 176 removed outlier: 4.099A pdb=" N THR D 170 " --> pdb=" O SER D 166 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG D 171 " --> pdb=" O PRO D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 256 removed outlier: 4.124A pdb=" N GLU D 256 " --> pdb=" O THR D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 287 removed outlier: 4.440A pdb=" N HIS D 287 " --> pdb=" O VAL D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 344 Processing helix chain 'D' and resid 353 through 360 Processing helix chain 'D' and resid 372 through 383 Processing helix chain 'D' and resid 383 through 392 removed outlier: 4.066A pdb=" N SER D 387 " --> pdb=" O ASP D 383 " (cutoff:3.500A) removed outlier: 4.133A 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 420 Processing helix chain 'D' and resid 439 through 445 removed outlier: 3.721A pdb=" N LEU D 445 " --> pdb=" O VAL D 442 " (cutoff:3.500A) 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 509 through 515 removed outlier: 3.940A pdb=" N TYR D 513 " --> pdb=" O LEU D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 535 through 543 removed outlier: 3.500A pdb=" N ASP D 538 " --> pdb=" O ILE D 535 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLY D 539 " --> pdb=" O VAL D 536 " (cutoff:3.500A) removed outlier: 4.032A 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 608 through 613 removed outlier: 3.652A pdb=" N SER D 612 " --> pdb=" O HIS D 608 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU D 613 " --> pdb=" O SER D 609 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 608 through 613' Processing helix chain 'D' and resid 629 through 638 removed outlier: 3.829A pdb=" N GLN D 636 " --> pdb=" O ILE D 633 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N HIS D 637 " --> pdb=" O SER D 634 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 660 removed outlier: 3.522A pdb=" N ILE D 658 " --> pdb=" O PRO D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 678 through 684 removed outlier: 3.770A 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 removed outlier: 3.757A pdb=" N GLY D 751 " --> pdb=" O SER D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 770 through 776 removed outlier: 3.618A 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 16 through 21 removed outlier: 3.572A pdb=" N ILE E 19 " --> pdb=" O ALA E 16 " (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 removed outlier: 3.511A pdb=" N LYS E 123 " --> pdb=" O HIS E 119 " (cutoff:3.500A) Proline residue: E 126 - end of helix removed outlier: 4.820A pdb=" N TRP E 143 " --> pdb=" O CYS E 139 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N PHE E 144 " --> pdb=" O SER E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 165 removed outlier: 3.840A pdb=" N LYS E 152 " --> pdb=" O ARG E 148 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP E 165 " --> pdb=" O LEU E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 176 removed outlier: 3.678A pdb=" N THR E 170 " --> pdb=" O SER E 166 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR E 176 " --> pdb=" O ALA E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 255 removed outlier: 3.525A 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 299 through 304 removed outlier: 3.787A pdb=" N THR E 303 " --> pdb=" O ILE E 299 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 344 Processing helix chain 'E' and resid 354 through 360 removed outlier: 3.622A pdb=" N GLU E 358 " --> pdb=" O GLU E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 372 through 383 Processing helix chain 'E' and resid 383 through 392 removed outlier: 4.439A pdb=" N SER E 387 " --> pdb=" O ASP E 383 " (cutoff:3.500A) removed outlier: 3.938A 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 419 Processing helix chain 'E' and resid 439 through 445 removed outlier: 3.562A pdb=" N LEU E 445 " --> pdb=" O VAL E 442 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 468 Processing helix chain 'E' and resid 484 through 494 removed outlier: 3.563A pdb=" N GLU E 493 " --> pdb=" O ALA E 489 " (cutoff:3.500A) Processing helix chain 'E' and resid 510 through 515 removed outlier: 3.942A pdb=" N TYR E 513 " --> pdb=" O LEU E 510 " (cutoff:3.500A) Processing helix chain 'E' and resid 537 through 543 removed outlier: 4.024A 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 613 removed outlier: 3.853A pdb=" N ILE E 610 " --> pdb=" O PRO E 607 " (cutoff:3.500A) Processing helix chain 'E' and resid 629 through 637 Processing helix chain 'E' and resid 655 through 661 removed outlier: 3.802A pdb=" N ILE E 658 " --> pdb=" O PRO E 655 " (cutoff:3.500A) Processing helix chain 'E' and resid 678 through 684 Processing helix chain 'E' and resid 701 through 707 Processing helix chain 'E' and resid 724 through 730 Processing helix chain 'E' and resid 747 through 753 removed outlier: 3.702A pdb=" N VAL E 750 " --> pdb=" O PRO E 747 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY E 751 " --> pdb=" O SER E 748 " (cutoff:3.500A) Processing helix chain 'E' and resid 770 through 776 removed outlier: 3.800A pdb=" N LEU E 773 " --> pdb=" O PRO E 770 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N CYS E 776 " --> pdb=" O LEU E 773 " (cutoff:3.500A) Processing helix chain 'E' and resid 787 through 792 Processing helix chain 'E' and resid 795 through 808 removed outlier: 3.663A pdb=" N GLU E 808 " --> pdb=" O ARG E 804 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 21 removed outlier: 3.855A pdb=" N ILE F 19 " --> pdb=" O ALA F 16 " (cutoff:3.500A) 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: 4.955A pdb=" N TRP F 143 " --> pdb=" O CYS F 139 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N PHE F 144 " --> pdb=" O SER F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 166 removed outlier: 4.348A pdb=" N LYS F 152 " --> pdb=" O ARG F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 176 removed outlier: 4.119A pdb=" N THR F 170 " --> pdb=" O SER F 166 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 256 removed outlier: 4.195A pdb=" N GLU F 256 " --> pdb=" O THR F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 287 removed outlier: 4.584A pdb=" N HIS F 287 " --> pdb=" O VAL F 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 343 Processing helix chain 'F' and resid 353 through 360 Processing helix chain 'F' and resid 372 through 383 Processing helix chain 'F' and resid 383 through 392 removed outlier: 4.191A pdb=" N SER F 387 " --> pdb=" O ASP F 383 " (cutoff:3.500A) removed outlier: 4.226A 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 420 Processing helix chain 'F' and resid 439 through 445 removed outlier: 3.799A 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 515 removed outlier: 3.775A pdb=" N TYR F 513 " --> pdb=" O LEU F 510 " (cutoff:3.500A) Processing helix chain 'F' and resid 535 through 543 removed outlier: 3.874A pdb=" N GLY F 539 " --> pdb=" O VAL F 536 " (cutoff:3.500A) removed outlier: 4.241A 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 611 Processing helix chain 'F' and resid 631 through 636 removed outlier: 3.719A pdb=" N GLN F 636 " --> pdb=" O ILE F 632 " (cutoff:3.500A) Processing helix chain 'F' and resid 655 through 660 removed outlier: 3.501A pdb=" N ILE F 658 " --> pdb=" O PRO F 655 " (cutoff:3.500A) Processing helix chain 'F' and resid 678 through 684 removed outlier: 3.590A pdb=" N LEU F 681 " --> pdb=" O PRO F 678 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N CYS F 684 " --> pdb=" O LEU F 681 " (cutoff:3.500A) Processing helix chain 'F' and resid 701 through 707 removed outlier: 3.621A 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: 3.803A pdb=" N GLY F 751 " --> pdb=" O SER F 748 " (cutoff:3.500A) Processing helix chain 'F' and resid 770 through 776 removed outlier: 3.579A pdb=" N CYS F 776 " --> pdb=" O LEU F 773 " (cutoff:3.500A) Processing helix chain 'F' and resid 787 through 792 Processing helix chain 'F' and resid 795 through 808 Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.613A pdb=" N LYS H 65 " --> pdb=" O ASP H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 108 through 112 removed outlier: 3.827A pdb=" N GLU H 111 " --> pdb=" O TYR H 108 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR H 112 " --> pdb=" O TYR H 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 108 through 112' Processing sheet with id=AA1, first strand: chain 'A' and resid 292 through 296 Processing sheet with id=AA2, first strand: chain 'A' and resid 421 through 422 removed outlier: 6.411A pdb=" N LEU A 428 " --> pdb=" O VAL A 450 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N LYS A 452 " --> pdb=" O LEU A 428 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LEU A 430 " --> pdb=" O LYS A 452 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N GLU A 454 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LEU A 432 " --> pdb=" O GLU A 454 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU A 451 " --> pdb=" O TRP A 475 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N TYR A 477 " --> pdb=" O LEU A 451 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N LEU A 453 " --> pdb=" O TYR A 477 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU A 474 " --> pdb=" O HIS A 499 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N LYS A 501 " --> pdb=" O LEU A 474 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU A 476 " --> pdb=" O LYS A 501 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU A 498 " --> pdb=" O HIS A 522 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N THR A 524 " --> pdb=" O LEU A 498 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE A 500 " --> pdb=" O THR A 524 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU A 549 " --> pdb=" O SER A 573 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N ASN A 575 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU A 551 " --> pdb=" O ASN A 575 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU A 572 " --> pdb=" O GLU A 597 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N ILE A 599 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE A 574 " --> pdb=" O ILE A 599 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE A 619 " --> pdb=" O LYS A 645 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N LEU A 713 " --> pdb=" O HIS A 737 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N LEU A 736 " --> pdb=" O GLU A 760 " (cutoff:3.500A) removed outlier: 7.047A 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 removed outlier: 6.389A pdb=" N VAL A 459 " --> pdb=" O LYS A 482 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 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 421 through 422 removed outlier: 6.824A pdb=" N LEU B 428 " --> pdb=" O VAL B 450 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N LYS B 452 " --> pdb=" O LEU B 428 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU B 430 " --> pdb=" O LYS B 452 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N GLU B 454 " --> pdb=" O LEU B 430 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU B 432 " --> pdb=" O GLU B 454 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LEU B 451 " --> pdb=" O TRP B 475 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N TYR B 477 " --> pdb=" O LEU B 451 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU B 453 " --> pdb=" O TYR B 477 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LEU B 549 " --> pdb=" O SER B 573 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ASN B 575 " --> pdb=" O LEU B 549 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU B 551 " --> pdb=" O ASN B 575 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU B 572 " --> pdb=" O GLU B 597 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ILE B 599 " --> pdb=" O LEU B 572 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N ILE B 574 " --> pdb=" O ILE B 599 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE B 619 " --> pdb=" O CYS B 643 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS B 645 " --> pdb=" O ILE B 619 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR B 668 " --> pdb=" O LEU B 644 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N LEU B 667 " --> pdb=" O ASP B 691 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU B 736 " --> pdb=" O GLU B 760 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE B 759 " --> pdb=" O VAL B 785 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 460 through 461 Processing sheet with id=AA7, first strand: chain 'C' and resid 53 through 56 Processing sheet with id=AA8, first strand: chain 'C' and resid 421 through 422 removed outlier: 6.139A pdb=" N LEU C 428 " --> pdb=" O VAL C 450 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N LYS C 452 " --> pdb=" O LEU C 428 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LEU C 430 " --> pdb=" O LYS C 452 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N GLU C 454 " --> pdb=" O LEU C 430 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LEU C 432 " --> pdb=" O GLU C 454 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU C 549 " --> pdb=" O SER C 573 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N ASN C 575 " --> pdb=" O LEU C 549 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LEU C 551 " --> pdb=" O ASN C 575 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU C 572 " --> pdb=" O GLU C 597 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N ILE C 599 " --> pdb=" O LEU C 572 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ILE C 574 " --> pdb=" O ILE C 599 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE C 619 " --> pdb=" O LYS C 645 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR C 668 " --> pdb=" O LEU C 644 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP C 691 " --> pdb=" O LEU C 667 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N LEU C 713 " --> pdb=" O HIS C 737 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU C 760 " --> pdb=" O LEU C 736 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE C 759 " --> pdb=" O VAL C 785 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 459 through 460 removed outlier: 6.325A pdb=" N VAL C 459 " --> pdb=" O LYS C 482 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 53 through 56 Processing sheet with id=AB2, first strand: chain 'D' and resid 60 through 61 Processing sheet with id=AB3, first strand: chain 'D' and resid 421 through 422 removed outlier: 6.467A pdb=" N LEU D 428 " --> pdb=" O VAL D 450 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N LYS D 452 " --> pdb=" O LEU D 428 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LEU D 430 " --> pdb=" O LYS D 452 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N GLU D 454 " --> pdb=" O LEU D 430 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU D 432 " --> pdb=" O GLU D 454 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LEU D 451 " --> pdb=" O TRP D 475 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N TYR D 477 " --> pdb=" O LEU D 451 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N LEU D 453 " --> pdb=" O TYR D 477 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LEU D 549 " --> pdb=" O SER D 573 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N ASN D 575 " --> pdb=" O LEU D 549 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU D 551 " --> pdb=" O ASN D 575 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU D 572 " --> pdb=" O GLU D 597 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ILE D 599 " --> pdb=" O LEU D 572 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N ILE D 574 " --> pdb=" O ILE D 599 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE D 619 " --> pdb=" O LYS D 645 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU D 644 " --> pdb=" O TYR D 668 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP D 691 " --> pdb=" O LEU D 667 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU D 713 " --> pdb=" O HIS D 737 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LEU D 736 " --> pdb=" O GLU D 760 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE D 759 " --> pdb=" O VAL D 785 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 460 through 461 Processing sheet with id=AB5, first strand: chain 'E' and resid 53 through 56 Processing sheet with id=AB6, first strand: chain 'E' and resid 421 through 422 removed outlier: 6.542A pdb=" N LEU E 451 " --> pdb=" O TRP E 475 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N TYR E 477 " --> pdb=" O LEU E 451 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N LEU E 453 " --> pdb=" O TYR E 477 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU E 549 " --> pdb=" O SER E 573 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N ASN E 575 " --> pdb=" O LEU E 549 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LEU E 551 " --> pdb=" O ASN E 575 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU E 572 " --> pdb=" O GLU E 597 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N ILE E 599 " --> pdb=" O LEU E 572 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ILE E 574 " --> pdb=" O ILE E 599 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ILE E 619 " --> pdb=" O LYS E 645 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR E 668 " --> pdb=" O LEU E 644 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N LEU E 713 " --> pdb=" O HIS E 737 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU E 760 " --> pdb=" O LEU E 736 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE E 759 " --> pdb=" O VAL E 785 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 459 through 461 removed outlier: 6.278A pdb=" N VAL E 459 " --> pdb=" O LYS E 482 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'F' and resid 53 through 56 Processing sheet with id=AB9, first strand: chain 'F' and resid 421 through 422 removed outlier: 6.283A pdb=" N LEU F 428 " --> pdb=" O VAL F 450 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N LYS F 452 " --> pdb=" O LEU F 428 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU F 430 " --> pdb=" O LYS F 452 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N GLU F 454 " --> pdb=" O LEU F 430 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU F 432 " --> pdb=" O GLU F 454 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU F 451 " --> pdb=" O TRP F 475 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N TYR F 477 " --> pdb=" O LEU F 451 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU F 453 " --> pdb=" O TYR F 477 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU F 474 " --> pdb=" O HIS F 499 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N LYS F 501 " --> pdb=" O LEU F 474 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU F 476 " --> pdb=" O LYS F 501 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N LEU F 549 " --> pdb=" O SER F 573 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N ASN F 575 " --> pdb=" O LEU F 549 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEU F 551 " --> pdb=" O ASN F 575 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU F 572 " --> pdb=" O GLU F 597 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ILE F 599 " --> pdb=" O LEU F 572 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ILE F 574 " --> pdb=" O ILE F 599 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE F 619 " --> pdb=" O LYS F 645 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU F 644 " --> pdb=" O TYR F 668 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP F 691 " --> pdb=" O LEU F 667 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N LEU F 690 " --> pdb=" O ALA F 714 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LEU F 713 " --> pdb=" O HIS F 737 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 460 through 461 Processing sheet with id=AC2, first strand: chain 'F' and resid 759 through 760 removed outlier: 6.278A pdb=" N ILE F 759 " --> pdb=" O VAL F 785 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AC4, first strand: chain 'G' and resid 10 through 13 removed outlier: 5.884A pdb=" N GLY G 10 " --> pdb=" O THR G 122 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N SER G 124 " --> pdb=" O GLY G 10 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N VAL G 12 " --> pdb=" O SER G 124 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TRP G 36 " --> pdb=" O ALA G 49 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.653A pdb=" N TYR G 114 " --> pdb=" O ALA G 98 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AC7, first strand: chain 'I' and resid 10 through 13 removed outlier: 5.981A pdb=" N GLY I 10 " --> pdb=" O THR I 122 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N SER I 124 " --> pdb=" O GLY I 10 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N VAL I 12 " --> pdb=" O SER I 124 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.652A pdb=" N TYR I 114 " --> pdb=" O ALA I 98 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AD1, first strand: chain 'H' and resid 11 through 13 removed outlier: 8.278A pdb=" N GLU H 32 " --> pdb=" O ALA H 52 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ALA H 52 " --> pdb=" O GLU H 32 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU H 34 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA H 50 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 11 through 13 removed outlier: 3.707A pdb=" N TYR H 114 " --> pdb=" O ALA H 98 " (cutoff:3.500A) 1756 hydrogen bonds defined for protein. 4434 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: 18.08 Time building geometry restraints manager: 15.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12145 1.34 - 1.46: 8946 1.46 - 1.58: 17966 1.58 - 1.70: 0 1.70 - 1.82: 216 Bond restraints: 39273 Sorted by residual: bond pdb=" CA TYR I 109 " pdb=" C TYR I 109 " ideal model delta sigma weight residual 1.523 1.500 0.023 1.80e-02 3.09e+03 1.62e+00 bond pdb=" CA TYR G 109 " pdb=" C TYR G 109 " ideal model delta sigma weight residual 1.523 1.501 0.022 1.80e-02 3.09e+03 1.55e+00 bond pdb=" N LEU F 700 " pdb=" CA LEU F 700 " ideal model delta sigma weight residual 1.463 1.448 0.015 1.22e-02 6.72e+03 1.44e+00 bond pdb=" CA ILE E 438 " pdb=" CB ILE E 438 " ideal model delta sigma weight residual 1.537 1.524 0.014 1.29e-02 6.01e+03 1.13e+00 bond pdb=" CA ILE A 438 " pdb=" CB ILE A 438 " ideal model delta sigma weight residual 1.537 1.524 0.013 1.29e-02 6.01e+03 1.04e+00 ... (remaining 39268 not shown) Histogram of bond angle deviations from ideal: 99.38 - 106.34: 948 106.34 - 113.30: 21913 113.30 - 120.26: 14300 120.26 - 127.21: 15620 127.21 - 134.17: 463 Bond angle restraints: 53244 Sorted by residual: angle pdb=" N PHE E 372 " pdb=" CA PHE E 372 " pdb=" C PHE E 372 " ideal model delta sigma weight residual 114.04 107.81 6.23 1.24e+00 6.50e-01 2.52e+01 angle pdb=" N VAL D 397 " pdb=" CA VAL D 397 " pdb=" C VAL D 397 " ideal model delta sigma weight residual 111.90 107.91 3.99 8.10e-01 1.52e+00 2.43e+01 angle pdb=" N ILE E 535 " pdb=" CA ILE E 535 " pdb=" C ILE E 535 " ideal model delta sigma weight residual 112.96 108.71 4.25 1.00e+00 1.00e+00 1.80e+01 angle pdb=" N ILE C 535 " pdb=" CA ILE C 535 " pdb=" C ILE C 535 " ideal model delta sigma weight residual 112.96 108.77 4.19 1.00e+00 1.00e+00 1.76e+01 angle pdb=" CA LEU F 584 " pdb=" CB LEU F 584 " pdb=" CG LEU F 584 " ideal model delta sigma weight residual 116.30 127.65 -11.35 3.50e+00 8.16e-02 1.05e+01 ... (remaining 53239 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 21644 17.46 - 34.92: 1626 34.92 - 52.38: 342 52.38 - 69.84: 66 69.84 - 87.30: 19 Dihedral angle restraints: 23697 sinusoidal: 9813 harmonic: 13884 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 -43.03 -42.97 1 1.00e+01 1.00e-02 2.58e+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 -44.81 -41.19 1 1.00e+01 1.00e-02 2.38e+01 dihedral pdb=" CB CYS B 57 " pdb=" SG CYS B 57 " pdb=" SG CYS B 65 " pdb=" CB CYS B 65 " ideal model delta sinusoidal sigma weight residual -86.00 -47.04 -38.96 1 1.00e+01 1.00e-02 2.14e+01 ... (remaining 23694 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 3191 0.027 - 0.053: 1851 0.053 - 0.080: 709 0.080 - 0.106: 234 0.106 - 0.133: 111 Chirality restraints: 6096 Sorted by residual: chirality pdb=" CA ILE B 677 " pdb=" N ILE B 677 " pdb=" C ILE B 677 " pdb=" CB ILE B 677 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.41e-01 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 2.57 -0.13 2.00e-01 2.50e+01 4.37e-01 chirality pdb=" CA ILE E 677 " pdb=" N ILE E 677 " pdb=" C ILE E 677 " pdb=" CB ILE E 677 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.36e-01 ... (remaining 6093 not shown) Planarity restraints: 6615 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 724 " -0.027 5.00e-02 4.00e+02 4.12e-02 2.72e+00 pdb=" N PRO C 725 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO C 725 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 725 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO E 724 " -0.024 5.00e-02 4.00e+02 3.61e-02 2.08e+00 pdb=" N PRO E 725 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO E 725 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO E 725 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER D 395 " -0.006 2.00e-02 2.50e+03 1.16e-02 1.36e+00 pdb=" C SER D 395 " 0.020 2.00e-02 2.50e+03 pdb=" O SER D 395 " -0.007 2.00e-02 2.50e+03 pdb=" N GLU D 396 " -0.007 2.00e-02 2.50e+03 ... (remaining 6612 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 939 2.68 - 3.24: 40166 3.24 - 3.79: 64404 3.79 - 4.35: 84709 4.35 - 4.90: 136453 Nonbonded interactions: 326671 Sorted by model distance: nonbonded pdb=" OE1 GLN G 39 " pdb=" OH TYR G 95 " model vdw 2.130 2.440 nonbonded pdb=" OD2 ASP E 102 " pdb=" OH TYR F 106 " model vdw 2.154 2.440 nonbonded pdb=" OH TYR B 351 " pdb=" OD2 ASP B 380 " model vdw 2.161 2.440 nonbonded pdb=" OD1 ASN C 554 " pdb=" OG1 THR C 579 " model vdw 2.164 2.440 nonbonded pdb=" OD2 ASP A 102 " pdb=" OH TYR B 106 " model vdw 2.167 2.440 ... (remaining 326666 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: 2.090 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: 0.040 Extract box with map and model: 11.360 Check model and map are aligned: 0.570 Set scattering table: 0.330 Process input model: 92.410 Find NCS groups from input model: 2.710 Set up NCS constraints: 0.280 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6739 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 : 0.004 0.030 39273 Z= 0.253 Angle : 0.553 11.352 53244 Z= 0.307 Chirality : 0.040 0.133 6096 Planarity : 0.003 0.041 6615 Dihedral : 13.063 87.299 14628 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer Outliers : 5.44 % 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: 4638 helix: 0.12 (0.12), residues: 2034 sheet: -0.93 (0.19), residues: 768 loop : -0.26 (0.15), residues: 1836 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 856 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 623 time to evaluate : 4.400 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 233 outliers final: 60 residues processed: 825 average time/residue: 0.5330 time to fit residues: 700.9568 Evaluate side-chains 309 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 249 time to evaluate : 4.425 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 0 residues processed: 60 average time/residue: 0.3411 time to fit residues: 45.1337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 390 optimal weight: 0.7980 chunk 350 optimal weight: 0.2980 chunk 194 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 chunk 236 optimal weight: 0.5980 chunk 187 optimal weight: 9.9990 chunk 362 optimal weight: 0.5980 chunk 140 optimal weight: 1.9990 chunk 220 optimal weight: 0.9980 chunk 269 optimal weight: 0.7980 chunk 419 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 592 ASN A 637 HIS A 709 ASN ** A 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 HIS ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 592 ASN B 637 HIS B 650 HIS ** B 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 694 HIS ** B 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 592 ASN C 637 HIS C 708 GLN ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 ASN D 478 HIS D 637 HIS E 105 GLN ** E 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 554 ASN E 650 HIS ** E 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 239 GLN F 467 GLN ** F 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 570 GLN F 592 ASN F 650 HIS G 30 GLN G 82 GLN I 82 GLN I 84 ASN H 3 GLN ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 39273 Z= 0.178 Angle : 0.608 13.492 53244 Z= 0.307 Chirality : 0.043 0.215 6096 Planarity : 0.004 0.083 6615 Dihedral : 4.190 16.319 5124 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer Outliers : 2.43 % 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 (0.12), residues: 4638 helix: 0.06 (0.11), residues: 2118 sheet: -0.68 (0.19), residues: 765 loop : -0.43 (0.15), residues: 1755 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 314 time to evaluate : 4.476 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: symmetry clash revert: symmetry clash outliers start: 104 outliers final: 33 residues processed: 402 average time/residue: 0.5112 time to fit residues: 336.0726 Evaluate side-chains 256 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 223 time to evaluate : 4.436 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.3479 time to fit residues: 27.5182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 233 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 349 optimal weight: 0.8980 chunk 285 optimal weight: 0.6980 chunk 115 optimal weight: 4.9990 chunk 420 optimal weight: 6.9990 chunk 454 optimal weight: 2.9990 chunk 374 optimal weight: 2.9990 chunk 416 optimal weight: 1.9990 chunk 143 optimal weight: 0.7980 chunk 337 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 592 ASN ** A 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 HIS ** B 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 729 GLN D 478 HIS D 592 ASN D 650 HIS ** E 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 672 ASN E 709 ASN ** E 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 650 HIS ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6787 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 39273 Z= 0.179 Angle : 0.546 10.939 53244 Z= 0.279 Chirality : 0.041 0.181 6096 Planarity : 0.004 0.064 6615 Dihedral : 4.082 17.571 5124 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer Outliers : 2.43 % 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: -0.46 (0.12), residues: 4638 helix: 0.06 (0.11), residues: 2121 sheet: -0.53 (0.19), residues: 756 loop : -0.42 (0.15), residues: 1761 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 262 time to evaluate : 4.285 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: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 104 outliers final: 42 residues processed: 353 average time/residue: 0.4834 time to fit residues: 286.9088 Evaluate side-chains 263 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 221 time to evaluate : 4.405 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 0 residues processed: 42 average time/residue: 0.3783 time to fit residues: 35.0821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 415 optimal weight: 9.9990 chunk 316 optimal weight: 0.8980 chunk 218 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 chunk 200 optimal weight: 2.9990 chunk 282 optimal weight: 0.5980 chunk 421 optimal weight: 9.9990 chunk 446 optimal weight: 0.8980 chunk 220 optimal weight: 0.6980 chunk 399 optimal weight: 7.9990 chunk 120 optimal weight: 7.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 ASN ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 HIS ** B 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 576 ASN ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 HIS D 637 HIS D 650 HIS ** E 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 467 GLN H 30 GLN ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 39273 Z= 0.205 Angle : 0.540 10.642 53244 Z= 0.276 Chirality : 0.041 0.292 6096 Planarity : 0.003 0.037 6615 Dihedral : 4.063 17.465 5124 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer Outliers : 2.03 % 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 (0.12), residues: 4638 helix: -0.01 (0.11), residues: 2151 sheet: -0.49 (0.19), residues: 759 loop : -0.51 (0.15), residues: 1728 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 250 time to evaluate : 4.378 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 outliers start: 87 outliers final: 31 residues processed: 322 average time/residue: 0.4746 time to fit residues: 259.6883 Evaluate side-chains 248 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 217 time to evaluate : 4.305 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.3828 time to fit residues: 28.4635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 371 optimal weight: 6.9990 chunk 253 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 chunk 332 optimal weight: 7.9990 chunk 184 optimal weight: 10.0000 chunk 381 optimal weight: 6.9990 chunk 308 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 228 optimal weight: 7.9990 chunk 400 optimal weight: 8.9990 chunk 112 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 657 GLN ** A 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 ASN ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 608 HIS ** B 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 592 ASN C 650 HIS ** C 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 HIS D 649 ASN D 663 ASN E 253 HIS E 312 HIS ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 592 ASN ** E 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 404 GLN F 467 GLN F 575 ASN F 614 HIS F 663 ASN H 30 GLN ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.4452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.088 39273 Z= 0.689 Angle : 0.953 11.842 53244 Z= 0.490 Chirality : 0.056 0.275 6096 Planarity : 0.007 0.065 6615 Dihedral : 5.714 30.153 5124 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 25.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer Outliers : 4.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.76 (0.12), residues: 4638 helix: -1.03 (0.10), residues: 2106 sheet: -0.93 (0.19), residues: 741 loop : -1.22 (0.14), residues: 1791 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 234 time to evaluate : 4.324 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 outliers start: 197 outliers final: 102 residues processed: 408 average time/residue: 0.4747 time to fit residues: 328.3446 Evaluate side-chains 295 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 193 time to evaluate : 4.551 Switching outliers to nearest non-outliers outliers start: 102 outliers final: 0 residues processed: 102 average time/residue: 0.3982 time to fit residues: 80.9854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 150 optimal weight: 0.9990 chunk 402 optimal weight: 0.9980 chunk 88 optimal weight: 0.6980 chunk 262 optimal weight: 4.9990 chunk 110 optimal weight: 0.7980 chunk 447 optimal weight: 5.9990 chunk 371 optimal weight: 1.9990 chunk 206 optimal weight: 8.9990 chunk 37 optimal weight: 0.9980 chunk 147 optimal weight: 8.9990 chunk 234 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 GLN ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 ASN A 637 HIS A 657 GLN A 660 ASN ** A 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 708 GLN B 718 ASN ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 HIS E 104 HIS ** E 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 467 GLN ** G 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 moved from start: 0.4398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 39273 Z= 0.201 Angle : 0.598 10.689 53244 Z= 0.306 Chirality : 0.043 0.242 6096 Planarity : 0.004 0.042 6615 Dihedral : 4.715 22.971 5124 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer Outliers : 1.80 % 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: -1.11 (0.12), residues: 4638 helix: -0.42 (0.11), residues: 2103 sheet: -0.76 (0.20), residues: 738 loop : -0.90 (0.15), residues: 1797 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 236 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: symmetry clash revert: symmetry clash outliers start: 77 outliers final: 34 residues processed: 301 average time/residue: 0.4878 time to fit residues: 250.7298 Evaluate side-chains 233 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 199 time to evaluate : 4.777 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.3334 time to fit residues: 27.4541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 430 optimal weight: 8.9990 chunk 50 optimal weight: 0.9980 chunk 254 optimal weight: 0.9990 chunk 326 optimal weight: 5.9990 chunk 252 optimal weight: 0.9990 chunk 376 optimal weight: 2.9990 chunk 249 optimal weight: 1.9990 chunk 445 optimal weight: 9.9990 chunk 278 optimal weight: 9.9990 chunk 271 optimal weight: 0.9990 chunk 205 optimal weight: 0.9980 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 HIS ** C 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 709 ASN ** C 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 650 HIS ** E 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 467 GLN F 650 HIS F 660 ASN ** G 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 120 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.4522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 39273 Z= 0.191 Angle : 0.570 11.140 53244 Z= 0.290 Chirality : 0.042 0.245 6096 Planarity : 0.004 0.042 6615 Dihedral : 4.453 21.753 5124 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer Outliers : 0.86 % 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: -0.92 (0.12), residues: 4638 helix: -0.26 (0.11), residues: 2103 sheet: -0.71 (0.20), residues: 738 loop : -0.77 (0.15), residues: 1797 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 225 time to evaluate : 4.488 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 outliers start: 37 outliers final: 19 residues processed: 253 average time/residue: 0.5173 time to fit residues: 221.5652 Evaluate side-chains 216 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 197 time to evaluate : 4.627 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.4023 time to fit residues: 19.9420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 275 optimal weight: 8.9990 chunk 177 optimal weight: 5.9990 chunk 265 optimal weight: 0.9980 chunk 134 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 86 optimal weight: 0.8980 chunk 283 optimal weight: 0.0970 chunk 303 optimal weight: 0.0170 chunk 220 optimal weight: 0.6980 chunk 41 optimal weight: 5.9990 chunk 350 optimal weight: 3.9990 overall best weight: 0.5416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 HIS C 132 HIS ** C 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 650 HIS ** E 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 404 GLN F 467 GLN ** G 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 120 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6839 moved from start: 0.4598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 39273 Z= 0.149 Angle : 0.537 9.547 53244 Z= 0.273 Chirality : 0.041 0.232 6096 Planarity : 0.003 0.041 6615 Dihedral : 4.169 18.625 5124 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer Outliers : 0.54 % 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: -0.71 (0.12), residues: 4638 helix: -0.08 (0.11), residues: 2100 sheet: -0.56 (0.20), residues: 726 loop : -0.70 (0.15), residues: 1812 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 230 time to evaluate : 4.144 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 outliers start: 23 outliers final: 11 residues processed: 246 average time/residue: 0.5016 time to fit residues: 208.7876 Evaluate side-chains 213 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 202 time to evaluate : 4.566 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.3642 time to fit residues: 13.8392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 405 optimal weight: 0.9990 chunk 426 optimal weight: 10.0000 chunk 389 optimal weight: 0.0970 chunk 414 optimal weight: 7.9990 chunk 249 optimal weight: 3.9990 chunk 180 optimal weight: 5.9990 chunk 325 optimal weight: 10.0000 chunk 127 optimal weight: 2.9990 chunk 374 optimal weight: 1.9990 chunk 392 optimal weight: 7.9990 chunk 413 optimal weight: 0.8980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 HIS ** C 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 650 HIS ** E 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 467 GLN ** G 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 120 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6879 moved from start: 0.4760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 39273 Z= 0.215 Angle : 0.567 10.027 53244 Z= 0.287 Chirality : 0.042 0.236 6096 Planarity : 0.004 0.045 6615 Dihedral : 4.256 19.850 5124 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer Outliers : 0.61 % 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: -0.77 (0.12), residues: 4638 helix: -0.15 (0.11), residues: 2106 sheet: -0.56 (0.20), residues: 726 loop : -0.73 (0.15), residues: 1806 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 204 time to evaluate : 4.468 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 outliers start: 26 outliers final: 10 residues processed: 223 average time/residue: 0.5312 time to fit residues: 202.2744 Evaluate side-chains 206 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 196 time to evaluate : 4.619 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.3831 time to fit residues: 13.1069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 272 optimal weight: 8.9990 chunk 438 optimal weight: 0.9980 chunk 267 optimal weight: 2.9990 chunk 208 optimal weight: 8.9990 chunk 305 optimal weight: 0.6980 chunk 460 optimal weight: 0.7980 chunk 423 optimal weight: 1.9990 chunk 366 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 283 optimal weight: 0.0980 chunk 224 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 HIS ** C 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.4847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 39273 Z= 0.170 Angle : 0.551 10.428 53244 Z= 0.277 Chirality : 0.041 0.224 6096 Planarity : 0.003 0.043 6615 Dihedral : 4.165 20.356 5124 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer Outliers : 0.30 % 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: -0.71 (0.12), residues: 4638 helix: -0.11 (0.11), residues: 2106 sheet: -0.54 (0.20), residues: 726 loop : -0.68 (0.15), residues: 1806 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 216 time to evaluate : 4.587 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 outliers start: 13 outliers final: 7 residues processed: 228 average time/residue: 0.5073 time to fit residues: 194.8007 Evaluate side-chains 205 residues out of total 4284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 198 time to evaluate : 4.504 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.4752 time to fit residues: 11.8110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 291 optimal weight: 0.5980 chunk 390 optimal weight: 0.9980 chunk 112 optimal weight: 0.3980 chunk 337 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 367 optimal weight: 0.1980 chunk 153 optimal weight: 0.0060 chunk 376 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 HIS ** C 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 650 HIS ** E 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.116879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.099059 restraints weight = 116794.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.099754 restraints weight = 179794.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.100144 restraints weight = 140859.790| |-----------------------------------------------------------------------------| r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6533 moved from start: 0.4915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.044 39273 Z= 0.139 Angle : 0.533 10.725 53244 Z= 0.268 Chirality : 0.041 0.250 6096 Planarity : 0.003 0.042 6615 Dihedral : 4.008 20.263 5124 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer Outliers : 0.19 % 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: -0.57 (0.12), residues: 4638 helix: 0.02 (0.12), residues: 2106 sheet: -0.48 (0.20), residues: 726 loop : -0.61 (0.15), residues: 1806 =============================================================================== Job complete usr+sys time: 6496.62 seconds wall clock time: 121 minutes 16.72 seconds (7276.72 seconds total)