Starting phenix.real_space_refine on Tue Apr 9 02:55:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sw7_40810/04_2024/8sw7_40810_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sw7_40810/04_2024/8sw7_40810.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sw7_40810/04_2024/8sw7_40810.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sw7_40810/04_2024/8sw7_40810.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sw7_40810/04_2024/8sw7_40810_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sw7_40810/04_2024/8sw7_40810_updated.pdb" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 102 5.16 5 C 9437 2.51 5 N 2600 2.21 5 O 2994 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 15133 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 3470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3470 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 20, 'TRANS': 419} Chain breaks: 3 Chain: "B" Number of atoms: 998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 998 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "C" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3424 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 20, 'TRANS': 412} Chain breaks: 4 Chain: "D" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 959 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "E" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 959 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "F" Number of atoms: 3365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3365 Classifications: {'peptide': 425} Link IDs: {'PTRANS': 18, 'TRANS': 406} Chain breaks: 5 Chain: "H" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 625 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 125} Link IDs: {'TRANS': 124} Unresolved non-hydrogen bonds: 250 Unresolved non-hydrogen angles: 375 Unresolved non-hydrogen dihedrals: 125 Planarities with less than four sites: {'UNK:plan-1': 125} Unresolved non-hydrogen planarities: 125 Chain: "L" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 530 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 106} Link IDs: {'TRANS': 105} Unresolved non-hydrogen bonds: 212 Unresolved non-hydrogen angles: 318 Unresolved non-hydrogen dihedrals: 106 Planarities with less than four sites: {'UNK:plan-1': 106} Unresolved non-hydrogen planarities: 106 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Time building chain proxies: 8.80, per 1000 atoms: 0.58 Number of scatterers: 15133 At special positions: 0 Unit cell: (128.875, 136.092, 120.627, 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 102 16.00 O 2994 8.00 N 2600 7.00 C 9437 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.02 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.02 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.04 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.01 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 73 " distance=2.02 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.05 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.02 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS E 605 " distance=2.05 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS D 605 " - pdb=" SG CYS F 501 " distance=2.10 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 73 " distance=2.03 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.04 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.02 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.06 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.02 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 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 133 " " NAG A 603 " - " ASN A 137 " " NAG A 604 " - " ASN A 156 " " NAG A 605 " - " ASN A 160 " " NAG A 606 " - " ASN A 197 " " NAG A 607 " - " ASN A 234 " " NAG A 608 " - " ASN A 241 " " NAG A 609 " - " ASN A 276 " " NAG A 610 " - " ASN A 289 " " NAG A 611 " - " ASN A 301 " " NAG A 612 " - " ASN A 332 " " NAG A 613 " - " ASN A 392 " " NAG A 614 " - " ASN A 448 " " NAG A 615 " - " ASN A 295 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 618 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 133 " " NAG C 603 " - " ASN C 156 " " NAG C 604 " - " ASN C 160 " " NAG C 605 " - " ASN C 234 " " NAG C 606 " - " ASN C 241 " " NAG C 607 " - " ASN C 289 " " NAG C 608 " - " ASN C 295 " " NAG C 609 " - " ASN C 301 " " NAG C 610 " - " ASN C 332 " " NAG C 611 " - " ASN C 392 " " NAG C 612 " - " ASN C 448 " " NAG C 613 " - " ASN C 386 " " NAG D 701 " - " ASN D 611 " " NAG D 702 " - " ASN D 637 " " NAG E 701 " - " ASN E 611 " " NAG E 702 " - " ASN E 618 " " NAG E 703 " - " ASN E 637 " " NAG F 601 " - " ASN F 88 " " NAG F 602 " - " ASN F 133 " " NAG F 603 " - " ASN F 156 " " NAG F 604 " - " ASN F 160 " " NAG F 605 " - " ASN F 234 " " NAG F 606 " - " ASN F 241 " " NAG F 607 " - " ASN F 276 " " NAG F 608 " - " ASN F 289 " " NAG F 609 " - " ASN F 295 " " NAG F 610 " - " ASN F 301 " " NAG F 611 " - " ASN F 332 " " NAG F 612 " - " ASN F 386 " " NAG F 613 " - " ASN F 392 " " NAG F 614 " - " ASN F 448 " " NAG G 1 " - " ASN A 262 " " NAG I 1 " - " ASN C 262 " " NAG J 1 " - " ASN F 262 " Time building additional restraints: 6.01 Conformation dependent library (CDL) restraints added in 2.6 seconds 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3578 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 39 helices and 37 sheets defined 24.8% alpha, 26.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.89 Creating SS restraints... Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 123 through 125 No H-bonds generated for 'chain 'A' and resid 123 through 125' Processing helix chain 'A' and resid 140 through 150 No H-bonds generated for 'chain 'A' and resid 140 through 150' Processing helix chain 'A' and resid 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 335 through 353 removed outlier: 4.123A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 372 No H-bonds generated for 'chain 'A' and resid 369 through 372' Processing helix chain 'A' and resid 475 through 485 removed outlier: 3.708A pdb=" N ARG A 480 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N SER A 481 " --> pdb=" O ASN A 478 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N TYR A 484 " --> pdb=" O SER A 481 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LYS A 485 " --> pdb=" O GLU A 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 527 removed outlier: 4.383A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 524 through 527' Processing helix chain 'B' and resid 530 through 543 removed outlier: 5.117A pdb=" N MET B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N THR B 536 " --> pdb=" O ALA B 532 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU B 537 " --> pdb=" O ALA B 533 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N THR B 538 " --> pdb=" O SER B 534 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N VAL B 539 " --> pdb=" O MET B 535 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 595 Processing helix chain 'B' and resid 612 through 614 No H-bonds generated for 'chain 'B' and resid 612 through 614' Processing helix chain 'B' and resid 620 through 623 No H-bonds generated for 'chain 'B' and resid 620 through 623' Processing helix chain 'B' and resid 628 through 634 Processing helix chain 'B' and resid 636 through 660 removed outlier: 5.295A pdb=" N GLN B 640 " --> pdb=" O ASN B 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 97 No H-bonds generated for 'chain 'C' and resid 95 through 97' Processing helix chain 'C' and resid 99 through 115 Processing helix chain 'C' and resid 123 through 125 No H-bonds generated for 'chain 'C' and resid 123 through 125' Processing helix chain 'C' and resid 178 through 180 No H-bonds generated for 'chain 'C' and resid 178 through 180' Processing helix chain 'C' and resid 335 through 352 removed outlier: 4.206A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 372 No H-bonds generated for 'chain 'C' and resid 369 through 372' Processing helix chain 'C' and resid 476 through 485 removed outlier: 4.489A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LYS C 485 " --> pdb=" O SER C 481 " (cutoff:3.500A) Processing helix chain 'D' and resid 530 through 541 removed outlier: 5.111A pdb=" N MET D 535 " --> pdb=" O GLY D 531 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N THR D 536 " --> pdb=" O ALA D 532 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LEU D 537 " --> pdb=" O ALA D 533 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N THR D 538 " --> pdb=" O SER D 534 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N VAL D 539 " --> pdb=" O MET D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 595 Processing helix chain 'D' and resid 619 through 624 Processing helix chain 'D' and resid 628 through 634 removed outlier: 3.529A pdb=" N LYS D 633 " --> pdb=" O LEU D 629 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU D 634 " --> pdb=" O GLN D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 662 removed outlier: 5.168A pdb=" N GLN D 640 " --> pdb=" O ASN D 637 " (cutoff:3.500A) Processing helix chain 'E' and resid 524 through 527 removed outlier: 4.178A pdb=" N GLY E 527 " --> pdb=" O GLY E 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 524 through 527' Processing helix chain 'E' and resid 533 through 542 removed outlier: 3.509A pdb=" N LEU E 537 " --> pdb=" O SER E 534 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N THR E 538 " --> pdb=" O MET E 535 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA E 541 " --> pdb=" O THR E 538 " (cutoff:3.500A) Processing helix chain 'E' and resid 573 through 595 Processing helix chain 'E' and resid 619 through 622 No H-bonds generated for 'chain 'E' and resid 619 through 622' Processing helix chain 'E' and resid 628 through 663 removed outlier: 5.855A pdb=" N ASN E 637 " --> pdb=" O LYS E 633 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N TYR E 638 " --> pdb=" O GLU E 634 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N THR E 639 " --> pdb=" O ILE E 635 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N GLN E 640 " --> pdb=" O SER E 636 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N ILE E 641 " --> pdb=" O ASN E 637 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU E 663 " --> pdb=" O ASP E 659 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 117 Processing helix chain 'F' and resid 164 through 166 No H-bonds generated for 'chain 'F' and resid 164 through 166' Processing helix chain 'F' and resid 178 through 180 No H-bonds generated for 'chain 'F' and resid 178 through 180' Processing helix chain 'F' and resid 335 through 352 removed outlier: 4.073A pdb=" N LYS F 351 " --> pdb=" O LYS F 347 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N HIS F 352 " --> pdb=" O GLN F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 372 No H-bonds generated for 'chain 'F' and resid 369 through 372' Processing helix chain 'F' and resid 477 through 485 removed outlier: 4.239A pdb=" N GLU F 482 " --> pdb=" O ASN F 478 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LYS F 485 " --> pdb=" O SER F 481 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing helix chain 'H' and resid 65 through 67 No H-bonds generated for 'chain 'H' and resid 65 through 67' Processing sheet with id= A, first strand: chain 'A' and resid 35 through 40 Processing sheet with id= B, first strand: chain 'A' and resid 45 through 47 Processing sheet with id= C, first strand: chain 'A' and resid 53 through 55 Processing sheet with id= D, first strand: chain 'A' and resid 91 through 94 Processing sheet with id= E, first strand: chain 'A' and resid 130 through 133 Processing sheet with id= F, first strand: chain 'A' and resid 181 through 183 Processing sheet with id= G, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.576A pdb=" N ALA A 433 " --> pdb=" O THR A 202 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'A' and resid 271 through 274 removed outlier: 6.904A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 443 through 449 removed outlier: 6.631A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 465 through 469 removed outlier: 6.372A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.108A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 35 through 40 Processing sheet with id= M, first strand: chain 'C' and resid 45 through 47 Processing sheet with id= N, first strand: chain 'C' and resid 53 through 55 Processing sheet with id= O, first strand: chain 'C' and resid 91 through 94 Processing sheet with id= P, first strand: chain 'C' and resid 172 through 177 Processing sheet with id= Q, first strand: chain 'C' and resid 201 through 203 removed outlier: 6.581A pdb=" N ALA C 433 " --> pdb=" O THR C 202 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.369A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N ALA C 362 " --> pdb=" O PRO C 470 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 374 through 378 removed outlier: 3.986A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.417A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 35 through 40 Processing sheet with id= V, first strand: chain 'F' and resid 45 through 47 removed outlier: 4.653A pdb=" N VAL F 242 " --> pdb=" O LEU F 86 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 53 through 55 Processing sheet with id= X, first strand: chain 'F' and resid 91 through 94 removed outlier: 3.877A pdb=" N GLU F 91 " --> pdb=" O CYS F 239 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'F' and resid 131 through 133 Processing sheet with id= Z, first strand: chain 'F' and resid 181 through 183 Processing sheet with id= AA, first strand: chain 'F' and resid 201 through 203 removed outlier: 6.518A pdb=" N ALA F 433 " --> pdb=" O THR F 202 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'F' and resid 271 through 273 removed outlier: 6.611A pdb=" N LEU F 260 " --> pdb=" O THR F 450 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 443 through 449 removed outlier: 7.511A pdb=" N GLN F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N SER F 334 " --> pdb=" O GLN F 293 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA F 329 " --> pdb=" O CYS F 418 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 382 through 384 removed outlier: 4.030A pdb=" N PHE F 382 " --> pdb=" O LYS F 421 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'F' and resid 304 through 312 removed outlier: 6.434A pdb=" N GLN F 315 " --> pdb=" O ILE F 309 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'H' and resid 18 through 21 Processing sheet with id= AG, first strand: chain 'H' and resid 119 through 121 removed outlier: 4.227A pdb=" N UNK H 34 " --> pdb=" O UNK H 51 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N UNK H 38 " --> pdb=" O UNK H 47 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N UNK H 47 " --> pdb=" O UNK H 38 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N UNK H 40 " --> pdb=" O UNK H 45 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N UNK H 45 " --> pdb=" O UNK H 40 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'L' and resid 4 through 6 Processing sheet with id= AI, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.638A pdb=" N UNK L 104 " --> pdb=" O UNK L 11 " (cutoff:3.500A) No H-bonds generated for sheet with id= AI Processing sheet with id= AJ, first strand: chain 'L' and resid 88 through 91 removed outlier: 5.369A pdb=" N UNK L 37 " --> pdb=" O UNK L 46 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N UNK L 46 " --> pdb=" O UNK L 37 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'H' and resid 97 through 99 removed outlier: 3.531A pdb=" N UNK H 114 " --> pdb=" O UNK H 98 " (cutoff:3.500A) 508 hydrogen bonds defined for protein. 1251 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: 5.02 Time building geometry restraints manager: 6.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.33: 3792 1.33 - 1.48: 5118 1.48 - 1.63: 6341 1.63 - 1.78: 52 1.78 - 1.94: 86 Bond restraints: 15389 Sorted by residual: bond pdb=" NE ARG F 504 " pdb=" CZ ARG F 504 " ideal model delta sigma weight residual 1.326 1.406 -0.080 1.10e-02 8.26e+03 5.24e+01 bond pdb=" NE ARG A 504 " pdb=" CZ ARG A 504 " ideal model delta sigma weight residual 1.326 1.399 -0.073 1.10e-02 8.26e+03 4.42e+01 bond pdb=" CD2 TRP E 571 " pdb=" CE3 TRP E 571 " ideal model delta sigma weight residual 1.398 1.504 -0.106 1.60e-02 3.91e+03 4.36e+01 bond pdb=" CD2 TRP D 571 " pdb=" CE3 TRP D 571 " ideal model delta sigma weight residual 1.398 1.500 -0.102 1.60e-02 3.91e+03 4.07e+01 bond pdb=" CZ2 TRP E 571 " pdb=" CH2 TRP E 571 " ideal model delta sigma weight residual 1.368 1.489 -0.121 1.90e-02 2.77e+03 4.03e+01 ... (remaining 15384 not shown) Histogram of bond angle deviations from ideal: 96.98 - 104.42: 217 104.42 - 111.87: 7244 111.87 - 119.32: 5998 119.32 - 126.76: 7204 126.76 - 134.21: 263 Bond angle restraints: 20926 Sorted by residual: angle pdb=" N PRO A 437 " pdb=" CA PRO A 437 " pdb=" C PRO A 437 " ideal model delta sigma weight residual 110.58 100.83 9.75 1.07e+00 8.73e-01 8.30e+01 angle pdb=" N ARG F 476 " pdb=" CA ARG F 476 " pdb=" C ARG F 476 " ideal model delta sigma weight residual 114.04 102.96 11.08 1.24e+00 6.50e-01 7.99e+01 angle pdb=" C ARG F 298 " pdb=" N PRO F 299 " pdb=" CA PRO F 299 " ideal model delta sigma weight residual 119.56 127.25 -7.69 1.01e+00 9.80e-01 5.79e+01 angle pdb=" C ARG A 298 " pdb=" N PRO A 299 " pdb=" CA PRO A 299 " ideal model delta sigma weight residual 119.56 127.19 -7.63 1.01e+00 9.80e-01 5.71e+01 angle pdb=" N PRO F 437 " pdb=" CA PRO F 437 " pdb=" C PRO F 437 " ideal model delta sigma weight residual 110.58 102.50 8.08 1.07e+00 8.73e-01 5.71e+01 ... (remaining 20921 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.13: 9708 21.13 - 42.27: 204 42.27 - 63.40: 70 63.40 - 84.54: 32 84.54 - 105.67: 15 Dihedral angle restraints: 10029 sinusoidal: 4537 harmonic: 5492 Sorted by residual: dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 174.83 -81.83 1 1.00e+01 1.00e-02 8.24e+01 dihedral pdb=" CB CYS F 126 " pdb=" SG CYS F 126 " pdb=" SG CYS F 196 " pdb=" CB CYS F 196 " ideal model delta sinusoidal sigma weight residual 93.00 140.08 -47.08 1 1.00e+01 1.00e-02 3.06e+01 dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual -86.00 -129.29 43.29 1 1.00e+01 1.00e-02 2.61e+01 ... (remaining 10026 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 1757 0.102 - 0.203: 526 0.203 - 0.304: 170 0.304 - 0.406: 97 0.406 - 0.507: 34 Chirality restraints: 2584 Sorted by residual: chirality pdb=" C1 BMA I 3 " pdb=" O4 NAG I 2 " pdb=" C2 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.52e+02 chirality pdb=" C1 BMA J 3 " pdb=" O4 NAG J 2 " pdb=" C2 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 1.04e+02 chirality pdb=" C1 BMA G 3 " pdb=" O4 NAG G 2 " pdb=" C2 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.84e+01 ... (remaining 2581 not shown) Planarity restraints: 2665 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN D 611 " -0.099 2.00e-02 2.50e+03 1.04e-01 1.35e+02 pdb=" CG ASN D 611 " 0.041 2.00e-02 2.50e+03 pdb=" OD1 ASN D 611 " 0.022 2.00e-02 2.50e+03 pdb=" ND2 ASN D 611 " 0.161 2.00e-02 2.50e+03 pdb=" C1 NAG D 701 " -0.126 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 234 " -0.095 2.00e-02 2.50e+03 9.81e-02 1.20e+02 pdb=" CG ASN A 234 " 0.045 2.00e-02 2.50e+03 pdb=" OD1 ASN A 234 " 0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN A 234 " 0.151 2.00e-02 2.50e+03 pdb=" C1 NAG A 607 " -0.119 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 133 " 0.076 2.00e-02 2.50e+03 7.89e-02 7.77e+01 pdb=" CG ASN C 133 " -0.036 2.00e-02 2.50e+03 pdb=" OD1 ASN C 133 " -0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN C 133 " -0.121 2.00e-02 2.50e+03 pdb=" C1 NAG C 602 " 0.096 2.00e-02 2.50e+03 ... (remaining 2662 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1886 2.73 - 3.27: 14070 3.27 - 3.82: 23445 3.82 - 4.36: 29646 4.36 - 4.90: 47937 Nonbonded interactions: 116984 Sorted by model distance: nonbonded pdb=" OG1 THR F 37 " pdb=" OG1 THR F 499 " model vdw 2.188 2.440 nonbonded pdb=" N UNK H 51 " pdb=" N UNK H 52 " model vdw 2.394 2.560 nonbonded pdb=" NZ LYS C 231 " pdb=" OE1 GLU C 267 " model vdw 2.418 2.520 nonbonded pdb=" N LEU F 125 " pdb=" O LEU F 125 " model vdw 2.419 2.496 nonbonded pdb=" N VAL F 127 " pdb=" O VAL F 127 " model vdw 2.423 2.496 ... (remaining 116979 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' and (resid 32 through 77 or resid 82 through 392 or resid 412 through \ 457 or resid 463 through 503 or resid 603 through 614)) selection = (chain 'C' and (resid 32 through 77 or resid 82 through 392 or resid 412 through \ 503 or resid 601 through 612)) selection = (chain 'F' and (resid 32 through 503 or resid 603 through 614)) } ncs_group { reference = (chain 'B' and (resid 522 through 664 or resid 701 through 702)) selection = chain 'D' selection = (chain 'E' and (resid 522 through 664 or resid 701 through 702)) } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' } 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 individual isotropic 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: 4.350 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: 0.000 Extract box with map and model: 12.030 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 43.860 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.110 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:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 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 : 0.022 0.145 15389 Z= 1.396 Angle : 1.718 11.084 20926 Z= 1.109 Chirality : 0.133 0.507 2584 Planarity : 0.009 0.052 2613 Dihedral : 11.373 105.669 6352 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 1.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.16 % Favored : 97.78 % Rotamer: Outliers : 0.14 % Allowed : 0.61 % Favored : 99.26 % 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 (0.20), residues: 1622 helix: 0.55 (0.26), residues: 376 sheet: 1.10 (0.25), residues: 398 loop : 0.33 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.009 TRP F 35 HIS 0.010 0.002 HIS C 374 PHE 0.029 0.006 PHE A 353 TYR 0.038 0.007 TYR B 643 ARG 0.009 0.001 ARG D 617 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 599 time to evaluate : 1.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 477 ASP cc_start: 0.7926 (m-30) cc_final: 0.7700 (m-30) REVERT: B 627 THR cc_start: 0.8679 (p) cc_final: 0.8456 (t) REVERT: F 474 ASP cc_start: 0.7602 (t70) cc_final: 0.7087 (t70) outliers start: 2 outliers final: 0 residues processed: 601 average time/residue: 0.3029 time to fit residues: 260.3358 Evaluate side-chains 368 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 368 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 157 optimal weight: 0.9990 chunk 141 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 146 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 109 optimal weight: 0.6980 chunk 169 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS A 103 GLN A 195 ASN A 203 GLN A 422 GLN A 425 ASN C 130 GLN C 287 GLN D 607 ASN ** E 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 591 GLN F 203 GLN F 283 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 15389 Z= 0.253 Angle : 0.727 15.852 20926 Z= 0.374 Chirality : 0.047 0.254 2584 Planarity : 0.005 0.085 2613 Dihedral : 8.109 68.971 3206 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.98 % Allowed : 12.86 % Favored : 84.16 % 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: 0.36 (0.21), residues: 1622 helix: 0.93 (0.27), residues: 369 sheet: 0.59 (0.24), residues: 441 loop : -0.21 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 479 HIS 0.005 0.001 HIS A 249 PHE 0.032 0.002 PHE F 53 TYR 0.036 0.002 TYR E 643 ARG 0.007 0.001 ARG F 298 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 432 time to evaluate : 1.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 477 ASP cc_start: 0.7878 (m-30) cc_final: 0.7652 (m-30) REVERT: B 616 ASN cc_start: 0.7525 (t0) cc_final: 0.7262 (t0) REVERT: B 647 GLU cc_start: 0.7058 (tt0) cc_final: 0.6794 (tt0) REVERT: C 492 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7447 (mt-10) REVERT: E 542 ARG cc_start: 0.7850 (ttm170) cc_final: 0.7581 (ttm170) outliers start: 44 outliers final: 26 residues processed: 451 average time/residue: 0.2692 time to fit residues: 179.7006 Evaluate side-chains 404 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 378 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 381 GLU Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain F residue 173 TYR Chi-restraints excluded: chain F residue 439 ILE Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 499 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 94 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 141 optimal weight: 7.9990 chunk 115 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 170 optimal weight: 6.9990 chunk 183 optimal weight: 9.9990 chunk 151 optimal weight: 4.9990 chunk 168 optimal weight: 10.0000 chunk 57 optimal weight: 0.5980 chunk 136 optimal weight: 0.0980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 183 GLN A 258 GLN A 302 ASN A 422 GLN A 478 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 15389 Z= 0.349 Angle : 0.714 16.856 20926 Z= 0.364 Chirality : 0.048 0.312 2584 Planarity : 0.005 0.047 2613 Dihedral : 7.115 49.452 3206 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 4.81 % Allowed : 14.22 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.06 (0.21), residues: 1622 helix: 0.83 (0.28), residues: 355 sheet: 0.18 (0.23), residues: 464 loop : -0.50 (0.22), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 35 HIS 0.007 0.001 HIS A 72 PHE 0.021 0.002 PHE F 53 TYR 0.017 0.002 TYR A 173 ARG 0.008 0.001 ARG A 504 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 402 time to evaluate : 1.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.8827 (m100) cc_final: 0.8462 (m100) REVERT: B 540 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.6780 (mp10) REVERT: B 616 ASN cc_start: 0.7821 (t0) cc_final: 0.7614 (t0) REVERT: B 647 GLU cc_start: 0.7001 (tt0) cc_final: 0.6670 (tt0) REVERT: C 486 TYR cc_start: 0.8453 (m-80) cc_final: 0.8226 (m-80) REVERT: E 542 ARG cc_start: 0.7968 (ttm170) cc_final: 0.7622 (ttm170) REVERT: E 645 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8428 (mt) REVERT: E 655 LYS cc_start: 0.8241 (mmtp) cc_final: 0.7859 (mtpp) REVERT: F 46 LYS cc_start: 0.8457 (mttp) cc_final: 0.7956 (mttm) REVERT: F 192 ARG cc_start: 0.7695 (ptt180) cc_final: 0.7479 (ptt180) outliers start: 71 outliers final: 56 residues processed: 440 average time/residue: 0.2664 time to fit residues: 172.8098 Evaluate side-chains 419 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 361 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 649 SER Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 534 SER Chi-restraints excluded: chain E residue 645 LEU Chi-restraints excluded: chain E residue 649 SER Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 173 TYR Chi-restraints excluded: chain F residue 209 SER Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 439 ILE Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 447 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 168 optimal weight: 9.9990 chunk 127 optimal weight: 0.0370 chunk 88 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 81 optimal weight: 8.9990 chunk 114 optimal weight: 1.9990 chunk 170 optimal weight: 5.9990 chunk 180 optimal weight: 9.9990 chunk 89 optimal weight: 0.6980 chunk 161 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 overall best weight: 1.3062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN C 287 GLN F 283 ASN F 293 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.4069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 15389 Z= 0.254 Angle : 0.625 16.028 20926 Z= 0.316 Chirality : 0.045 0.186 2584 Planarity : 0.004 0.040 2613 Dihedral : 6.348 43.557 3206 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 4.54 % Allowed : 15.71 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.23 (0.21), residues: 1622 helix: 0.87 (0.28), residues: 356 sheet: 0.04 (0.23), residues: 464 loop : -0.67 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 35 HIS 0.004 0.001 HIS C 249 PHE 0.020 0.002 PHE F 53 TYR 0.018 0.002 TYR F 484 ARG 0.006 0.001 ARG F 178 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 367 time to evaluate : 1.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.8789 (m100) cc_final: 0.8436 (m100) REVERT: A 183 GLN cc_start: 0.7898 (OUTLIER) cc_final: 0.7658 (mm-40) REVERT: B 616 ASN cc_start: 0.7721 (t0) cc_final: 0.7500 (t0) REVERT: B 647 GLU cc_start: 0.7088 (tt0) cc_final: 0.6745 (tt0) REVERT: E 542 ARG cc_start: 0.7944 (ttm170) cc_final: 0.7682 (ttm170) REVERT: F 290 GLU cc_start: 0.7497 (tp30) cc_final: 0.7243 (tp30) outliers start: 67 outliers final: 54 residues processed: 408 average time/residue: 0.2612 time to fit residues: 158.7052 Evaluate side-chains 397 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 342 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 649 SER Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 534 SER Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain E residue 661 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 209 SER Chi-restraints excluded: chain F residue 369 LEU Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 446 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 150 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 134 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 154 optimal weight: 0.3980 chunk 124 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 162 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 283 ASN F 293 GLN F 478 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.4337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15389 Z= 0.271 Angle : 0.620 15.499 20926 Z= 0.314 Chirality : 0.044 0.202 2584 Planarity : 0.004 0.042 2613 Dihedral : 6.153 43.851 3206 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.60 % Allowed : 16.38 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.21), residues: 1622 helix: 1.00 (0.29), residues: 348 sheet: -0.13 (0.24), residues: 458 loop : -0.78 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP F 35 HIS 0.004 0.001 HIS A 330 PHE 0.018 0.002 PHE A 376 TYR 0.024 0.002 TYR E 643 ARG 0.005 0.001 ARG A 504 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 355 time to evaluate : 1.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.8809 (m100) cc_final: 0.8437 (m100) REVERT: A 102 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7474 (mm-30) REVERT: B 540 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.6703 (mp10) REVERT: B 647 GLU cc_start: 0.7093 (tt0) cc_final: 0.6765 (tt0) REVERT: C 175 LEU cc_start: 0.8542 (mp) cc_final: 0.8191 (mt) REVERT: E 542 ARG cc_start: 0.7932 (ttm170) cc_final: 0.7673 (ttm170) REVERT: F 231 LYS cc_start: 0.8156 (mmtp) cc_final: 0.7552 (mmtp) outliers start: 68 outliers final: 58 residues processed: 398 average time/residue: 0.2633 time to fit residues: 157.3977 Evaluate side-chains 396 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 337 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 649 SER Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 534 SER Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 209 SER Chi-restraints excluded: chain F residue 274 SER Chi-restraints excluded: chain F residue 293 GLN Chi-restraints excluded: chain F residue 369 LEU Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 450 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 60 optimal weight: 0.6980 chunk 162 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 180 optimal weight: 9.9990 chunk 150 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 15 optimal weight: 8.9990 chunk 59 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN C 195 ASN F 283 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.4541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 15389 Z= 0.214 Angle : 0.601 14.939 20926 Z= 0.304 Chirality : 0.044 0.212 2584 Planarity : 0.004 0.037 2613 Dihedral : 5.860 41.983 3206 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 4.20 % Allowed : 17.20 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.41 (0.21), residues: 1622 helix: 1.09 (0.29), residues: 349 sheet: -0.21 (0.24), residues: 459 loop : -0.87 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP F 35 HIS 0.003 0.001 HIS A 374 PHE 0.016 0.001 PHE F 53 TYR 0.014 0.001 TYR F 484 ARG 0.007 0.000 ARG F 178 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 360 time to evaluate : 1.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.8793 (m100) cc_final: 0.8442 (m100) REVERT: A 435 TYR cc_start: 0.8424 (t80) cc_final: 0.8163 (t80) REVERT: B 540 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.6635 (mp10) REVERT: B 647 GLU cc_start: 0.7082 (tt0) cc_final: 0.6774 (tt0) REVERT: D 610 TRP cc_start: 0.7459 (t-100) cc_final: 0.7092 (t-100) REVERT: E 542 ARG cc_start: 0.7902 (ttm170) cc_final: 0.7645 (ttm170) REVERT: F 231 LYS cc_start: 0.8172 (mmtp) cc_final: 0.7581 (mmtp) outliers start: 62 outliers final: 50 residues processed: 397 average time/residue: 0.2625 time to fit residues: 154.4183 Evaluate side-chains 390 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 339 time to evaluate : 1.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 649 SER Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 274 SER Chi-restraints excluded: chain F residue 369 LEU Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 427 TRP Chi-restraints excluded: chain F residue 499 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 174 optimal weight: 10.0000 chunk 20 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 132 optimal weight: 7.9990 chunk 102 optimal weight: 1.9990 chunk 152 optimal weight: 5.9990 chunk 101 optimal weight: 0.7980 chunk 180 optimal weight: 10.0000 chunk 112 optimal weight: 0.9980 chunk 109 optimal weight: 0.7980 chunk 83 optimal weight: 8.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN A 374 HIS ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN F 283 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.4763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15389 Z= 0.221 Angle : 0.581 14.645 20926 Z= 0.296 Chirality : 0.043 0.207 2584 Planarity : 0.004 0.041 2613 Dihedral : 5.723 42.139 3206 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.67 % Allowed : 17.60 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 (0.21), residues: 1622 helix: 1.14 (0.29), residues: 348 sheet: -0.24 (0.24), residues: 448 loop : -0.94 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP F 35 HIS 0.007 0.001 HIS A 72 PHE 0.015 0.002 PHE A 376 TYR 0.014 0.001 TYR C 486 ARG 0.007 0.000 ARG F 178 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 347 time to evaluate : 1.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.8807 (m100) cc_final: 0.8440 (m100) REVERT: A 51 THR cc_start: 0.8942 (m) cc_final: 0.8724 (p) REVERT: A 102 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7545 (mm-30) REVERT: A 435 TYR cc_start: 0.8376 (t80) cc_final: 0.8132 (t80) REVERT: B 540 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.6647 (mp10) REVERT: B 647 GLU cc_start: 0.7119 (tt0) cc_final: 0.6813 (tt0) REVERT: E 542 ARG cc_start: 0.7891 (ttm170) cc_final: 0.7625 (ttm170) REVERT: F 107 ASP cc_start: 0.7654 (m-30) cc_final: 0.7254 (m-30) REVERT: F 191 TYR cc_start: 0.6098 (OUTLIER) cc_final: 0.5250 (p90) REVERT: F 231 LYS cc_start: 0.8195 (mmtp) cc_final: 0.7571 (mmtp) outliers start: 69 outliers final: 56 residues processed: 387 average time/residue: 0.2585 time to fit residues: 150.1424 Evaluate side-chains 397 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 339 time to evaluate : 1.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 649 SER Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 173 TYR Chi-restraints excluded: chain F residue 191 TYR Chi-restraints excluded: chain F residue 209 SER Chi-restraints excluded: chain F residue 274 SER Chi-restraints excluded: chain F residue 300 ASN Chi-restraints excluded: chain F residue 369 LEU Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 504 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 111 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 114 optimal weight: 0.8980 chunk 122 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 141 optimal weight: 0.8980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN ** C 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 283 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.4883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15389 Z= 0.240 Angle : 0.591 13.963 20926 Z= 0.301 Chirality : 0.044 0.197 2584 Planarity : 0.004 0.039 2613 Dihedral : 5.744 42.791 3206 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 4.67 % Allowed : 18.35 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 (0.21), residues: 1622 helix: 1.15 (0.29), residues: 348 sheet: -0.27 (0.24), residues: 462 loop : -1.02 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP F 112 HIS 0.003 0.001 HIS A 330 PHE 0.015 0.002 PHE A 376 TYR 0.015 0.001 TYR C 486 ARG 0.007 0.000 ARG F 178 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 354 time to evaluate : 1.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.8787 (m100) cc_final: 0.8414 (m100) REVERT: A 51 THR cc_start: 0.8950 (m) cc_final: 0.8719 (p) REVERT: A 102 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7496 (mm-30) REVERT: A 435 TYR cc_start: 0.8349 (t80) cc_final: 0.8117 (t80) REVERT: B 540 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.6694 (mp10) REVERT: B 647 GLU cc_start: 0.7106 (tt0) cc_final: 0.6786 (tt0) REVERT: E 542 ARG cc_start: 0.7896 (ttm170) cc_final: 0.7658 (ttm170) REVERT: F 107 ASP cc_start: 0.7656 (m-30) cc_final: 0.7259 (m-30) REVERT: F 191 TYR cc_start: 0.6345 (OUTLIER) cc_final: 0.5454 (p90) outliers start: 69 outliers final: 63 residues processed: 393 average time/residue: 0.2542 time to fit residues: 149.4371 Evaluate side-chains 410 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 345 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 191 TYR Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 649 SER Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 173 TYR Chi-restraints excluded: chain F residue 191 TYR Chi-restraints excluded: chain F residue 209 SER Chi-restraints excluded: chain F residue 274 SER Chi-restraints excluded: chain F residue 288 LEU Chi-restraints excluded: chain F residue 300 ASN Chi-restraints excluded: chain F residue 369 LEU Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 504 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 163 optimal weight: 0.7980 chunk 172 optimal weight: 10.0000 chunk 157 optimal weight: 3.9990 chunk 167 optimal weight: 10.0000 chunk 101 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 131 optimal weight: 0.0070 chunk 51 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 chunk 158 optimal weight: 0.0570 chunk 110 optimal weight: 0.9980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN F 283 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.5002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15389 Z= 0.161 Angle : 0.553 14.010 20926 Z= 0.280 Chirality : 0.042 0.180 2584 Planarity : 0.003 0.039 2613 Dihedral : 5.404 43.853 3206 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.99 % Allowed : 19.70 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.40 (0.21), residues: 1622 helix: 1.23 (0.29), residues: 349 sheet: -0.13 (0.25), residues: 442 loop : -0.98 (0.21), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP F 112 HIS 0.004 0.001 HIS C 352 PHE 0.013 0.001 PHE A 361 TYR 0.011 0.001 TYR A 173 ARG 0.007 0.000 ARG F 178 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 363 time to evaluate : 1.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.8767 (m100) cc_final: 0.8428 (m100) REVERT: A 102 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7516 (mm-30) REVERT: A 435 TYR cc_start: 0.8269 (t80) cc_final: 0.8056 (t80) REVERT: B 540 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.6682 (mp10) REVERT: C 192 ARG cc_start: 0.7337 (tpt170) cc_final: 0.7093 (tpt170) REVERT: C 348 GLN cc_start: 0.8151 (tp40) cc_final: 0.7718 (tp40) REVERT: F 107 ASP cc_start: 0.7645 (m-30) cc_final: 0.7244 (m-30) REVERT: F 231 LYS cc_start: 0.8156 (mmtp) cc_final: 0.7605 (mmtp) outliers start: 59 outliers final: 51 residues processed: 394 average time/residue: 0.2619 time to fit residues: 155.9525 Evaluate side-chains 403 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 351 time to evaluate : 1.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 649 SER Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 173 TYR Chi-restraints excluded: chain F residue 209 SER Chi-restraints excluded: chain F residue 288 LEU Chi-restraints excluded: chain F residue 300 ASN Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain F residue 504 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 177 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 123 optimal weight: 3.9990 chunk 186 optimal weight: 10.0000 chunk 171 optimal weight: 8.9990 chunk 148 optimal weight: 0.7980 chunk 15 optimal weight: 7.9990 chunk 114 optimal weight: 0.6980 chunk 90 optimal weight: 3.9990 chunk 117 optimal weight: 0.9980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN C 170 GLN F 283 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.5085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 15389 Z= 0.332 Angle : 0.647 13.929 20926 Z= 0.327 Chirality : 0.046 0.210 2584 Planarity : 0.004 0.040 2613 Dihedral : 5.968 44.553 3206 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.79 % Allowed : 20.72 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.60 (0.21), residues: 1622 helix: 1.02 (0.29), residues: 354 sheet: -0.23 (0.25), residues: 436 loop : -1.11 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP F 112 HIS 0.007 0.001 HIS C 352 PHE 0.030 0.002 PHE A 361 TYR 0.014 0.002 TYR F 484 ARG 0.007 0.001 ARG F 178 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 354 time to evaluate : 1.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.8849 (m100) cc_final: 0.8494 (m100) REVERT: A 102 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7562 (mm-30) REVERT: D 599 SER cc_start: 0.8765 (t) cc_final: 0.8540 (p) REVERT: F 46 LYS cc_start: 0.8014 (mttp) cc_final: 0.7804 (mttp) REVERT: F 107 ASP cc_start: 0.7738 (m-30) cc_final: 0.7358 (m-30) REVERT: F 166 ARG cc_start: 0.6251 (mmp80) cc_final: 0.5901 (mmp-170) outliers start: 56 outliers final: 52 residues processed: 390 average time/residue: 0.2774 time to fit residues: 161.8507 Evaluate side-chains 389 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 337 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 649 SER Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 173 TYR Chi-restraints excluded: chain F residue 209 SER Chi-restraints excluded: chain F residue 300 ASN Chi-restraints excluded: chain F residue 369 LEU Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain F residue 504 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 158 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 148 optimal weight: 0.0370 chunk 62 optimal weight: 2.9990 chunk 152 optimal weight: 0.4980 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 0.0980 chunk 130 optimal weight: 3.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN ** C 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 283 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.163796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.138003 restraints weight = 23519.343| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 3.53 r_work: 0.3559 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.5193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15389 Z= 0.162 Angle : 0.579 14.000 20926 Z= 0.293 Chirality : 0.043 0.224 2584 Planarity : 0.004 0.039 2613 Dihedral : 5.608 44.485 3206 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.84 % Allowed : 21.87 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.43 (0.21), residues: 1622 helix: 1.25 (0.29), residues: 348 sheet: -0.16 (0.25), residues: 440 loop : -1.00 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP F 112 HIS 0.005 0.001 HIS C 352 PHE 0.021 0.001 PHE F 391 TYR 0.013 0.001 TYR A 191 ARG 0.008 0.000 ARG F 178 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3956.72 seconds wall clock time: 72 minutes 59.96 seconds (4379.96 seconds total)