Starting phenix.real_space_refine on Wed Jul 24 01:44:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4b_41026/07_2024/8t4b_41026.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4b_41026/07_2024/8t4b_41026.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4b_41026/07_2024/8t4b_41026.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4b_41026/07_2024/8t4b_41026.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4b_41026/07_2024/8t4b_41026.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4b_41026/07_2024/8t4b_41026.cif" } resolution = 3.5 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= 0.032 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 147 5.16 5 C 15429 2.51 5 N 4074 2.21 5 O 4875 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" Residue "E PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 24525 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 3445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3445 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 21, 'TRANS': 412} Chain breaks: 4 Chain: "C" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 937 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "D" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 789 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "B" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 950 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "H" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 942 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 8, 'TRANS': 116} Chain: "L" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 805 Classifications: {'peptide': 105} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 96} Chain: "E" Number of atoms: 3445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3445 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 21, 'TRANS': 412} Chain breaks: 4 Chain: "J" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 937 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "M" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 789 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "G" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 950 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "O" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 942 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 8, 'TRANS': 116} Chain: "Q" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 805 Classifications: {'peptide': 105} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 96} Chain: "F" Number of atoms: 3445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3445 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 21, 'TRANS': 412} Chain breaks: 4 Chain: "K" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 937 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "N" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 789 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "I" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 950 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "P" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 942 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 8, 'TRANS': 116} Chain: "R" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 805 Classifications: {'peptide': 105} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 96} Chain: "S" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "T" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "U" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "V" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "W" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "X" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" 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: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" 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: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" 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: "I" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 14.44, per 1000 atoms: 0.59 Number of scatterers: 24525 At special positions: 0 Unit cell: (142.6, 151.8, 174.8, 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 147 16.00 O 4875 8.00 N 4074 7.00 C 15429 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.05 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 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 C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.05 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.04 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS G 605 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 598 " - pdb=" SG CYS G 604 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.05 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=2.04 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 501 " - pdb=" SG CYS I 605 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 598 " - pdb=" SG CYS I 604 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 92 " distance=2.04 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA S 3 " - " MAN S 4 " " BMA T 3 " - " MAN T 4 " " BMA U 3 " - " MAN U 4 " " BMA V 3 " - " MAN V 4 " " BMA W 3 " - " MAN W 4 " " BMA X 3 " - " MAN X 4 " ALPHA1-6 " BMA S 3 " - " MAN S 5 " " BMA U 3 " - " MAN U 5 " " BMA W 3 " - " MAN W 5 " BETA1-4 " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " NAG-ASN " NAG A 601 " - " ASN A 289 " " NAG A 602 " - " ASN A 301 " " NAG A 603 " - " ASN A 88 " " 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 276 " " NAG A 609 " - " ASN A 295 " " NAG A 610 " - " ASN A 339 " " NAG A 611 " - " ASN A 386 " " NAG A 612 " - " ASN A 448 " " NAG A 613 " - " ASN A 241 " " NAG B 701 " - " ASN B 611 " " NAG E 601 " - " ASN E 289 " " NAG E 602 " - " ASN E 301 " " NAG E 603 " - " ASN E 88 " " NAG E 604 " - " ASN E 156 " " NAG E 605 " - " ASN E 160 " " NAG E 606 " - " ASN E 197 " " NAG E 607 " - " ASN E 234 " " NAG E 608 " - " ASN E 276 " " NAG E 609 " - " ASN E 295 " " NAG E 610 " - " ASN E 339 " " NAG E 611 " - " ASN E 386 " " NAG E 612 " - " ASN E 448 " " NAG E 613 " - " ASN E 241 " " NAG F 601 " - " ASN F 289 " " NAG F 602 " - " ASN F 301 " " NAG F 603 " - " ASN F 88 " " NAG F 604 " - " ASN F 156 " " NAG F 605 " - " ASN F 160 " " NAG F 606 " - " ASN F 197 " " NAG F 607 " - " ASN F 234 " " NAG F 608 " - " ASN F 276 " " NAG F 609 " - " ASN F 295 " " NAG F 610 " - " ASN F 339 " " NAG F 611 " - " ASN F 386 " " NAG F 612 " - " ASN F 448 " " NAG F 613 " - " ASN F 241 " " NAG G 701 " - " ASN G 611 " " NAG I 701 " - " ASN I 611 " " NAG S 1 " - " ASN A 332 " " NAG T 1 " - " ASN A 262 " " NAG U 1 " - " ASN E 332 " " NAG V 1 " - " ASN E 262 " " NAG W 1 " - " ASN F 332 " " NAG X 1 " - " ASN F 262 " Time building additional restraints: 10.33 Conformation dependent library (CDL) restraints added in 4.4 seconds 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5562 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 48 sheets defined 19.6% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.81 Creating SS restraints... Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 194 through 199 removed outlier: 4.184A pdb=" N THR A 198 " --> pdb=" O ILE A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.681A pdb=" N THR A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 391 removed outlier: 3.531A pdb=" N PHE A 391 " --> pdb=" O SER A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 429 removed outlier: 4.157A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 484 removed outlier: 4.080A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 61 through 64 Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'D' and resid 79 through 83 removed outlier: 4.058A pdb=" N GLU D 83 " --> pdb=" O ALA D 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.423A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.665A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 595 Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 635 removed outlier: 3.582A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 661 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 100B through 100F Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'E' and resid 96 through 98 No H-bonds generated for 'chain 'E' and resid 96 through 98' Processing helix chain 'E' and resid 99 through 117 Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 194 through 199 removed outlier: 4.184A pdb=" N THR E 198 " --> pdb=" O ILE E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 350 Processing helix chain 'E' and resid 351 through 353 No H-bonds generated for 'chain 'E' and resid 351 through 353' Processing helix chain 'E' and resid 368 through 373 removed outlier: 3.681A pdb=" N THR E 373 " --> pdb=" O LEU E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 391 removed outlier: 3.531A pdb=" N PHE E 391 " --> pdb=" O SER E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 429 removed outlier: 4.157A pdb=" N GLN E 428 " --> pdb=" O ASN E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 484 removed outlier: 4.080A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'J' and resid 61 through 64 Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'M' and resid 79 through 83 removed outlier: 4.057A pdb=" N GLU M 83 " --> pdb=" O ALA M 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 523 through 528 removed outlier: 4.423A pdb=" N GLY G 527 " --> pdb=" O GLY G 524 " (cutoff:3.500A) Processing helix chain 'G' and resid 529 through 534 Processing helix chain 'G' and resid 536 through 542 removed outlier: 3.665A pdb=" N GLN G 540 " --> pdb=" O THR G 536 " (cutoff:3.500A) Processing helix chain 'G' and resid 573 through 595 Processing helix chain 'G' and resid 618 through 625 Processing helix chain 'G' and resid 627 through 635 removed outlier: 3.582A pdb=" N LYS G 633 " --> pdb=" O LEU G 629 " (cutoff:3.500A) Processing helix chain 'G' and resid 638 through 661 Processing helix chain 'O' and resid 28 through 32 Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'O' and resid 100B through 100F Processing helix chain 'Q' and resid 79 through 83 Processing helix chain 'F' and resid 96 through 98 No H-bonds generated for 'chain 'F' and resid 96 through 98' Processing helix chain 'F' and resid 99 through 117 Processing helix chain 'F' and resid 122 through 126 Processing helix chain 'F' and resid 194 through 199 removed outlier: 4.184A pdb=" N THR F 198 " --> pdb=" O ILE F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 350 Processing helix chain 'F' and resid 351 through 353 No H-bonds generated for 'chain 'F' and resid 351 through 353' Processing helix chain 'F' and resid 368 through 373 removed outlier: 3.681A pdb=" N THR F 373 " --> pdb=" O LEU F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 387 through 391 removed outlier: 3.531A pdb=" N PHE F 391 " --> pdb=" O SER F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 429 removed outlier: 4.157A pdb=" N GLN F 428 " --> pdb=" O ASN F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 484 removed outlier: 4.080A pdb=" N SER F 481 " --> pdb=" O ASP F 477 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N GLU F 482 " --> pdb=" O ASN F 478 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 32 Processing helix chain 'K' and resid 61 through 64 Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'N' and resid 79 through 83 removed outlier: 4.057A pdb=" N GLU N 83 " --> pdb=" O ALA N 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 523 through 528 removed outlier: 4.423A pdb=" N GLY I 527 " --> pdb=" O GLY I 524 " (cutoff:3.500A) Processing helix chain 'I' and resid 529 through 534 Processing helix chain 'I' and resid 536 through 542 removed outlier: 3.665A pdb=" N GLN I 540 " --> pdb=" O THR I 536 " (cutoff:3.500A) Processing helix chain 'I' and resid 573 through 595 Processing helix chain 'I' and resid 618 through 625 Processing helix chain 'I' and resid 627 through 635 removed outlier: 3.582A pdb=" N LYS I 633 " --> pdb=" O LEU I 629 " (cutoff:3.500A) Processing helix chain 'I' and resid 638 through 661 Processing helix chain 'P' and resid 28 through 32 Processing helix chain 'P' and resid 83 through 87 Processing helix chain 'P' and resid 100B through 100F Processing helix chain 'R' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.185A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.813A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.725A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 172 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.381A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 312 removed outlier: 7.077A pdb=" N ASN A 301 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N VAL A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 315 through 323 current: chain 'A' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 381 through 385 current: chain 'A' and resid 465 through 469 Processing sheet with id=AA8, first strand: chain 'C' and resid 3 through 6 removed outlier: 3.842A pdb=" N GLY C 16 " --> pdb=" O SER C 82B" (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 34 through 39 removed outlier: 5.751A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 57 through 59 current: chain 'C' and resid 100H through 103 Processing sheet with id=AB1, first strand: chain 'D' and resid 19 through 24 Processing sheet with id=AB2, first strand: chain 'D' and resid 33 through 38 removed outlier: 6.468A pdb=" N TRP D 35 " --> pdb=" O MET D 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 45 through 48 current: chain 'D' and resid 95A through 98 Processing sheet with id=AB3, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB4, first strand: chain 'H' and resid 33 through 39 removed outlier: 6.580A pdb=" N TRP H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N TYR H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 59 current: chain 'H' and resid 102 through 103 Processing sheet with id=AB5, first strand: chain 'H' and resid 98 through 99 Processing sheet with id=AB6, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB7, first strand: chain 'L' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 10 through 12 current: chain 'L' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 53 through 54 current: chain 'L' and resid 97 through 98 Processing sheet with id=AB8, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.185A pdb=" N VAL G 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N VAL E 38 " --> pdb=" O THR G 606 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N THR G 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N TYR E 40 " --> pdb=" O CYS G 604 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N CYS G 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.812A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AC2, first strand: chain 'E' and resid 91 through 94 removed outlier: 3.725A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 172 through 177 Processing sheet with id=AC4, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.382A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 259 through 261 current: chain 'E' and resid 284 through 312 removed outlier: 7.077A pdb=" N ASN E 301 " --> pdb=" O VAL E 323 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N VAL E 323 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 315 through 323 current: chain 'E' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 381 through 385 current: chain 'E' and resid 465 through 469 Processing sheet with id=AC6, first strand: chain 'J' and resid 3 through 6 removed outlier: 3.843A pdb=" N GLY J 16 " --> pdb=" O SER J 82B" (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 34 through 39 removed outlier: 5.750A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 57 through 59 current: chain 'J' and resid 100H through 103 Processing sheet with id=AC8, first strand: chain 'M' and resid 19 through 24 Processing sheet with id=AC9, first strand: chain 'M' and resid 33 through 38 removed outlier: 6.469A pdb=" N TRP M 35 " --> pdb=" O MET M 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 45 through 48 current: chain 'M' and resid 95A through 98 Processing sheet with id=AD1, first strand: chain 'O' and resid 3 through 7 Processing sheet with id=AD2, first strand: chain 'O' and resid 33 through 39 removed outlier: 6.580A pdb=" N TRP O 34 " --> pdb=" O TYR O 50 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N TYR O 50 " --> pdb=" O TRP O 34 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N TRP O 36 " --> pdb=" O ILE O 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 57 through 59 current: chain 'O' and resid 102 through 103 Processing sheet with id=AD3, first strand: chain 'O' and resid 98 through 99 Processing sheet with id=AD4, first strand: chain 'Q' and resid 4 through 7 Processing sheet with id=AD5, first strand: chain 'Q' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 10 through 12 current: chain 'Q' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 53 through 54 current: chain 'Q' and resid 97 through 98 Processing sheet with id=AD6, first strand: chain 'F' and resid 494 through 499 removed outlier: 5.186A pdb=" N VAL I 608 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N VAL F 38 " --> pdb=" O THR I 606 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N THR I 606 " --> pdb=" O VAL F 38 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N TYR F 40 " --> pdb=" O CYS I 604 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N CYS I 604 " --> pdb=" O TYR F 40 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 45 through 47 removed outlier: 3.813A pdb=" N ILE F 225 " --> pdb=" O VAL F 245 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 53 through 55 Processing sheet with id=AD9, first strand: chain 'F' and resid 91 through 94 removed outlier: 3.725A pdb=" N GLU F 91 " --> pdb=" O CYS F 239 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 172 through 177 Processing sheet with id=AE2, first strand: chain 'F' and resid 201 through 203 removed outlier: 6.382A pdb=" N THR F 202 " --> pdb=" O TYR F 435 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 259 through 261 current: chain 'F' and resid 284 through 312 removed outlier: 7.077A pdb=" N ASN F 301 " --> pdb=" O VAL F 323 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N VAL F 323 " --> pdb=" O ASN F 301 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N THR F 303 " --> pdb=" O GLY F 321 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N GLN F 315 " --> pdb=" O ILE F 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 315 through 323 current: chain 'F' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 381 through 385 current: chain 'F' and resid 465 through 469 Processing sheet with id=AE4, first strand: chain 'K' and resid 3 through 6 removed outlier: 3.842A pdb=" N GLY K 16 " --> pdb=" O SER K 82B" (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 34 through 39 removed outlier: 5.751A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 57 through 59 current: chain 'K' and resid 100H through 103 Processing sheet with id=AE6, first strand: chain 'N' and resid 19 through 24 Processing sheet with id=AE7, first strand: chain 'N' and resid 33 through 38 removed outlier: 6.468A pdb=" N TRP N 35 " --> pdb=" O MET N 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 45 through 48 current: chain 'N' and resid 95A through 98 Processing sheet with id=AE8, first strand: chain 'P' and resid 3 through 7 Processing sheet with id=AE9, first strand: chain 'P' and resid 33 through 39 removed outlier: 6.580A pdb=" N TRP P 34 " --> pdb=" O TYR P 50 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N TYR P 50 " --> pdb=" O TRP P 34 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N TRP P 36 " --> pdb=" O ILE P 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 57 through 59 current: chain 'P' and resid 102 through 103 Processing sheet with id=AF1, first strand: chain 'P' and resid 98 through 99 Processing sheet with id=AF2, first strand: chain 'R' and resid 4 through 7 Processing sheet with id=AF3, first strand: chain 'R' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 10 through 12 current: chain 'R' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 53 through 54 current: chain 'R' and resid 97 through 98 699 hydrogen bonds defined for protein. 1728 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: 8.40 Time building geometry restraints manager: 11.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7708 1.34 - 1.47: 6546 1.47 - 1.60: 10604 1.60 - 1.72: 0 1.72 - 1.85: 201 Bond restraints: 25059 Sorted by residual: bond pdb=" CG PRO Q 80 " pdb=" CD PRO Q 80 " ideal model delta sigma weight residual 1.503 1.303 0.200 3.40e-02 8.65e+02 3.47e+01 bond pdb=" CG PRO L 80 " pdb=" CD PRO L 80 " ideal model delta sigma weight residual 1.503 1.303 0.200 3.40e-02 8.65e+02 3.47e+01 bond pdb=" CG PRO R 80 " pdb=" CD PRO R 80 " ideal model delta sigma weight residual 1.503 1.303 0.200 3.40e-02 8.65e+02 3.46e+01 bond pdb=" CB CYS E 331 " pdb=" SG CYS E 331 " ideal model delta sigma weight residual 1.808 1.727 0.081 3.30e-02 9.18e+02 6.02e+00 bond pdb=" CB CYS F 331 " pdb=" SG CYS F 331 " ideal model delta sigma weight residual 1.808 1.727 0.081 3.30e-02 9.18e+02 6.00e+00 ... (remaining 25054 not shown) Histogram of bond angle deviations from ideal: 92.65 - 100.96: 30 100.96 - 109.27: 3111 109.27 - 117.57: 15752 117.57 - 125.88: 14569 125.88 - 134.19: 564 Bond angle restraints: 34026 Sorted by residual: angle pdb=" CA PRO Q 80 " pdb=" N PRO Q 80 " pdb=" CD PRO Q 80 " ideal model delta sigma weight residual 112.00 97.83 14.17 1.40e+00 5.10e-01 1.03e+02 angle pdb=" CA PRO R 80 " pdb=" N PRO R 80 " pdb=" CD PRO R 80 " ideal model delta sigma weight residual 112.00 97.83 14.17 1.40e+00 5.10e-01 1.03e+02 angle pdb=" CA PRO L 80 " pdb=" N PRO L 80 " pdb=" CD PRO L 80 " ideal model delta sigma weight residual 112.00 97.86 14.14 1.40e+00 5.10e-01 1.02e+02 angle pdb=" N PRO L 80 " pdb=" CD PRO L 80 " pdb=" CG PRO L 80 " ideal model delta sigma weight residual 103.20 92.65 10.55 1.50e+00 4.44e-01 4.94e+01 angle pdb=" N PRO R 80 " pdb=" CD PRO R 80 " pdb=" CG PRO R 80 " ideal model delta sigma weight residual 103.20 92.66 10.54 1.50e+00 4.44e-01 4.93e+01 ... (remaining 34021 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.53: 15054 21.53 - 43.06: 522 43.06 - 64.59: 144 64.59 - 86.12: 45 86.12 - 107.64: 27 Dihedral angle restraints: 15792 sinusoidal: 7092 harmonic: 8700 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 92 " pdb=" CB CYS H 92 " ideal model delta sinusoidal sigma weight residual 93.00 42.86 50.14 1 1.00e+01 1.00e-02 3.45e+01 dihedral pdb=" CB CYS O 22 " pdb=" SG CYS O 22 " pdb=" SG CYS O 92 " pdb=" CB CYS O 92 " ideal model delta sinusoidal sigma weight residual 93.00 42.88 50.12 1 1.00e+01 1.00e-02 3.45e+01 dihedral pdb=" CB CYS P 22 " pdb=" SG CYS P 22 " pdb=" SG CYS P 92 " pdb=" CB CYS P 92 " ideal model delta sinusoidal sigma weight residual 93.00 42.88 50.12 1 1.00e+01 1.00e-02 3.44e+01 ... (remaining 15789 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.171: 3939 0.171 - 0.343: 30 0.343 - 0.514: 0 0.514 - 0.685: 3 0.685 - 0.857: 3 Chirality restraints: 3975 Sorted by residual: chirality pdb=" C1 NAG F 607 " pdb=" ND2 ASN F 234 " pdb=" C2 NAG F 607 " pdb=" O5 NAG F 607 " both_signs ideal model delta sigma weight residual False -2.40 -1.54 -0.86 2.00e-01 2.50e+01 1.83e+01 chirality pdb=" C1 NAG E 607 " pdb=" ND2 ASN E 234 " pdb=" C2 NAG E 607 " pdb=" O5 NAG E 607 " both_signs ideal model delta sigma weight residual False -2.40 -1.54 -0.86 2.00e-01 2.50e+01 1.83e+01 chirality pdb=" C1 NAG A 607 " pdb=" ND2 ASN A 234 " pdb=" C2 NAG A 607 " pdb=" O5 NAG A 607 " both_signs ideal model delta sigma weight residual False -2.40 -1.55 -0.85 2.00e-01 2.50e+01 1.82e+01 ... (remaining 3972 not shown) Planarity restraints: 4287 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN R 79 " -0.099 5.00e-02 4.00e+02 1.38e-01 3.05e+01 pdb=" N PRO R 80 " 0.238 5.00e-02 4.00e+02 pdb=" CA PRO R 80 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO R 80 " -0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN L 79 " -0.099 5.00e-02 4.00e+02 1.38e-01 3.05e+01 pdb=" N PRO L 80 " 0.238 5.00e-02 4.00e+02 pdb=" CA PRO L 80 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO L 80 " -0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN Q 79 " -0.099 5.00e-02 4.00e+02 1.38e-01 3.04e+01 pdb=" N PRO Q 80 " 0.238 5.00e-02 4.00e+02 pdb=" CA PRO Q 80 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO Q 80 " -0.075 5.00e-02 4.00e+02 ... (remaining 4284 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 3395 2.76 - 3.30: 22450 3.30 - 3.83: 39817 3.83 - 4.37: 48129 4.37 - 4.90: 82373 Nonbonded interactions: 196164 Sorted by model distance: nonbonded pdb=" NH2 ARG E 500 " pdb=" OG SER J 98 " model vdw 2.227 2.520 nonbonded pdb=" NH2 ARG A 500 " pdb=" OG SER C 98 " model vdw 2.228 2.520 nonbonded pdb=" NH2 ARG F 500 " pdb=" OG SER K 98 " model vdw 2.228 2.520 nonbonded pdb=" NH1 ARG R 61 " pdb=" O SER R 77 " model vdw 2.265 2.520 nonbonded pdb=" NH1 ARG L 61 " pdb=" O SER L 77 " model vdw 2.265 2.520 ... (remaining 196159 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'C' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'H' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'L' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = chain 'S' selection = chain 'U' selection = chain 'W' } ncs_group { reference = chain 'T' selection = chain 'V' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.060 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 67.230 Find NCS groups from input model: 2.540 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 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 : 0.007 0.200 25059 Z= 0.477 Angle : 1.086 14.175 34026 Z= 0.593 Chirality : 0.065 0.857 3975 Planarity : 0.007 0.138 4239 Dihedral : 13.170 107.645 10095 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 1.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.34 % Allowed : 5.30 % Favored : 94.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.88 (0.15), residues: 2973 helix: 0.56 (0.26), residues: 357 sheet: 0.80 (0.17), residues: 942 loop : 0.61 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP O 34 HIS 0.010 0.001 HIS F 374 PHE 0.054 0.004 PHE A 320 TYR 0.043 0.003 TYR H 50 ARG 0.005 0.001 ARG P 66 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 391 time to evaluate : 2.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 ASN cc_start: 0.8449 (t0) cc_final: 0.8187 (t0) REVERT: D 42 LYS cc_start: 0.7750 (mmmm) cc_final: 0.7516 (mtpt) REVERT: B 657 GLU cc_start: 0.8495 (tp30) cc_final: 0.8236 (mt-10) REVERT: H 72 ASP cc_start: 0.6771 (t0) cc_final: 0.6138 (t0) REVERT: H 75 GLU cc_start: 0.7777 (mp0) cc_final: 0.7367 (mp0) REVERT: E 434 MET cc_start: 0.8182 (ttt) cc_final: 0.7743 (ttt) REVERT: J 28 THR cc_start: 0.8789 (p) cc_final: 0.8406 (p) REVERT: J 72 ASP cc_start: 0.7981 (t0) cc_final: 0.7687 (t0) REVERT: M 50 ASP cc_start: 0.8358 (t70) cc_final: 0.7673 (t0) REVERT: M 91 TYR cc_start: 0.9006 (t80) cc_final: 0.8756 (t80) REVERT: O 72 ASP cc_start: 0.7105 (t0) cc_final: 0.6419 (t0) REVERT: O 75 GLU cc_start: 0.8047 (mp0) cc_final: 0.7455 (mp0) REVERT: Q 73 LEU cc_start: 0.8236 (tp) cc_final: 0.8023 (tp) REVERT: F 434 MET cc_start: 0.8261 (ttt) cc_final: 0.7794 (ttt) REVERT: K 28 THR cc_start: 0.8820 (p) cc_final: 0.8486 (p) REVERT: K 52 ASP cc_start: 0.8683 (p0) cc_final: 0.8362 (p0) REVERT: K 72 ASP cc_start: 0.7777 (t0) cc_final: 0.7496 (t0) REVERT: N 50 ASP cc_start: 0.8040 (t70) cc_final: 0.7741 (t0) REVERT: I 607 ASN cc_start: 0.8067 (m-40) cc_final: 0.7857 (m-40) REVERT: I 647 GLU cc_start: 0.7595 (tt0) cc_final: 0.7163 (tt0) REVERT: P 72 ASP cc_start: 0.6894 (t0) cc_final: 0.6114 (t0) REVERT: P 75 GLU cc_start: 0.8020 (mp0) cc_final: 0.7507 (mp0) REVERT: R 69 THR cc_start: 0.7586 (p) cc_final: 0.6986 (p) outliers start: 9 outliers final: 5 residues processed: 397 average time/residue: 0.3722 time to fit residues: 225.3340 Evaluate side-chains 260 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 255 time to evaluate : 2.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain E residue 188 ASN Chi-restraints excluded: chain F residue 88 ASN Chi-restraints excluded: chain F residue 188 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 250 optimal weight: 4.9990 chunk 225 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 151 optimal weight: 0.8980 chunk 120 optimal weight: 0.8980 chunk 232 optimal weight: 2.9990 chunk 90 optimal weight: 9.9990 chunk 141 optimal weight: 1.9990 chunk 173 optimal weight: 0.5980 chunk 269 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN L 37 GLN L 90 GLN ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 183 GLN M 79 GLN O 39 GLN Q 37 GLN Q 90 GLN F 183 GLN K 3 GLN R 37 GLN ** R 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 25059 Z= 0.250 Angle : 0.609 8.879 34026 Z= 0.319 Chirality : 0.047 0.374 3975 Planarity : 0.004 0.047 4239 Dihedral : 9.470 80.996 4684 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.95 % Favored : 97.95 % Rotamer: Outliers : 1.83 % Allowed : 7.25 % Favored : 90.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.15), residues: 2973 helix: 2.03 (0.28), residues: 372 sheet: 1.05 (0.16), residues: 963 loop : 0.22 (0.15), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 479 HIS 0.007 0.001 HIS A 374 PHE 0.027 0.002 PHE F 320 TYR 0.026 0.002 TYR R 49 ARG 0.007 0.001 ARG N 94 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 272 time to evaluate : 2.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 28 THR cc_start: 0.8854 (p) cc_final: 0.8441 (p) REVERT: C 72 ASP cc_start: 0.7898 (t0) cc_final: 0.7637 (t0) REVERT: D 78 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8251 (mp) REVERT: H 72 ASP cc_start: 0.6596 (t0) cc_final: 0.6139 (t0) REVERT: H 75 GLU cc_start: 0.7764 (mp0) cc_final: 0.7382 (mp0) REVERT: L 78 LEU cc_start: 0.8291 (tt) cc_final: 0.8039 (tt) REVERT: J 28 THR cc_start: 0.8736 (OUTLIER) cc_final: 0.8292 (p) REVERT: J 72 ASP cc_start: 0.8007 (t0) cc_final: 0.7719 (t0) REVERT: M 50 ASP cc_start: 0.8320 (t70) cc_final: 0.7652 (t0) REVERT: M 91 TYR cc_start: 0.8974 (t80) cc_final: 0.8764 (t80) REVERT: O 37 ILE cc_start: 0.9209 (mm) cc_final: 0.8974 (mm) REVERT: O 72 ASP cc_start: 0.6940 (t0) cc_final: 0.6382 (t0) REVERT: O 75 GLU cc_start: 0.7874 (mp0) cc_final: 0.7633 (mp0) REVERT: Q 78 LEU cc_start: 0.8147 (tt) cc_final: 0.7787 (tt) REVERT: F 434 MET cc_start: 0.8773 (ttt) cc_final: 0.8246 (ttt) REVERT: K 28 THR cc_start: 0.8769 (OUTLIER) cc_final: 0.8313 (p) REVERT: K 72 ASP cc_start: 0.7829 (t0) cc_final: 0.7450 (t0) REVERT: N 50 ASP cc_start: 0.8215 (t70) cc_final: 0.7843 (t0) REVERT: I 530 MET cc_start: 0.8356 (mtp) cc_final: 0.8133 (mtp) REVERT: I 607 ASN cc_start: 0.8154 (m-40) cc_final: 0.7948 (m-40) REVERT: P 46 GLU cc_start: 0.8157 (tt0) cc_final: 0.7809 (tt0) REVERT: P 72 ASP cc_start: 0.6871 (t0) cc_final: 0.6363 (t0) REVERT: P 75 GLU cc_start: 0.7916 (mp0) cc_final: 0.7480 (mp0) outliers start: 48 outliers final: 26 residues processed: 298 average time/residue: 0.3321 time to fit residues: 160.5674 Evaluate side-chains 265 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 236 time to evaluate : 2.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 53 GLN Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain Q residue 23 CYS Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain F residue 88 ASN Chi-restraints excluded: chain K residue 3 GLN Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain R residue 94 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 149 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 224 optimal weight: 1.9990 chunk 183 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 270 optimal weight: 2.9990 chunk 291 optimal weight: 0.3980 chunk 240 optimal weight: 1.9990 chunk 267 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 216 optimal weight: 0.8980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 25059 Z= 0.313 Angle : 0.594 8.549 34026 Z= 0.309 Chirality : 0.046 0.324 3975 Planarity : 0.004 0.033 4239 Dihedral : 8.405 75.731 4678 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.99 % Favored : 96.97 % Rotamer: Outliers : 2.14 % Allowed : 7.82 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.82 (0.15), residues: 2973 helix: 2.27 (0.29), residues: 372 sheet: 0.91 (0.17), residues: 975 loop : -0.04 (0.15), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 479 HIS 0.008 0.001 HIS D 39 PHE 0.031 0.002 PHE E 320 TYR 0.023 0.002 TYR Q 49 ARG 0.005 0.001 ARG N 94 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 248 time to evaluate : 2.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 28 THR cc_start: 0.8819 (p) cc_final: 0.8400 (p) REVERT: C 72 ASP cc_start: 0.7990 (t0) cc_final: 0.7699 (t0) REVERT: H 72 ASP cc_start: 0.6560 (t0) cc_final: 0.6021 (t0) REVERT: H 75 GLU cc_start: 0.7765 (mp0) cc_final: 0.7353 (mp0) REVERT: E 434 MET cc_start: 0.8821 (ttt) cc_final: 0.8615 (ttt) REVERT: J 28 THR cc_start: 0.8723 (p) cc_final: 0.8330 (p) REVERT: J 72 ASP cc_start: 0.8058 (t0) cc_final: 0.7726 (t0) REVERT: M 50 ASP cc_start: 0.8265 (t70) cc_final: 0.7618 (t0) REVERT: M 74 THR cc_start: 0.8104 (m) cc_final: 0.7377 (p) REVERT: M 91 TYR cc_start: 0.9039 (t80) cc_final: 0.8820 (t80) REVERT: O 72 ASP cc_start: 0.6917 (t0) cc_final: 0.6311 (t0) REVERT: O 75 GLU cc_start: 0.7837 (mp0) cc_final: 0.7580 (mp0) REVERT: Q 78 LEU cc_start: 0.8344 (tt) cc_final: 0.8009 (tt) REVERT: F 125 LEU cc_start: 0.9180 (mt) cc_final: 0.8908 (tp) REVERT: F 426 MET cc_start: 0.8438 (mmm) cc_final: 0.8155 (mtp) REVERT: F 434 MET cc_start: 0.8757 (ttt) cc_final: 0.8287 (ttt) REVERT: F 475 MET cc_start: 0.8325 (tpp) cc_final: 0.8082 (tpp) REVERT: K 28 THR cc_start: 0.8839 (p) cc_final: 0.8399 (p) REVERT: K 72 ASP cc_start: 0.7932 (t0) cc_final: 0.7536 (t0) REVERT: K 97 MET cc_start: 0.8498 (ttm) cc_final: 0.8285 (ttm) REVERT: N 50 ASP cc_start: 0.8315 (t70) cc_final: 0.7968 (t0) REVERT: P 46 GLU cc_start: 0.8046 (tt0) cc_final: 0.7609 (tt0) REVERT: P 72 ASP cc_start: 0.6951 (t0) cc_final: 0.6456 (t0) REVERT: P 75 GLU cc_start: 0.7803 (mp0) cc_final: 0.7271 (mp0) REVERT: R 78 LEU cc_start: 0.8476 (tt) cc_final: 0.8152 (tt) outliers start: 56 outliers final: 36 residues processed: 293 average time/residue: 0.3298 time to fit residues: 156.7574 Evaluate side-chains 263 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 227 time to evaluate : 2.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 97 MET Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain G residue 612 SER Chi-restraints excluded: chain G residue 616 ASN Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain Q residue 23 CYS Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain F residue 88 ASN Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 52 THR Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain I residue 612 SER Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 94 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 266 optimal weight: 1.9990 chunk 203 optimal weight: 3.9990 chunk 140 optimal weight: 0.4980 chunk 29 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 181 optimal weight: 4.9990 chunk 271 optimal weight: 2.9990 chunk 287 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 256 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- 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** D 31 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 79 GLN ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 25059 Z= 0.450 Angle : 0.655 14.608 34026 Z= 0.340 Chirality : 0.047 0.299 3975 Planarity : 0.004 0.035 4239 Dihedral : 8.259 72.159 4678 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.75 % Allowed : 7.97 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.29 (0.15), residues: 2973 helix: 1.94 (0.28), residues: 372 sheet: 0.51 (0.17), residues: 936 loop : -0.37 (0.14), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP J 103 HIS 0.008 0.001 HIS F 330 PHE 0.035 0.002 PHE A 320 TYR 0.025 0.002 TYR L 49 ARG 0.005 0.001 ARG B 617 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 246 time to evaluate : 3.046 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: C 28 THR cc_start: 0.8857 (p) cc_final: 0.8434 (p) REVERT: C 72 ASP cc_start: 0.8118 (t0) cc_final: 0.7803 (t0) REVERT: D 95 THR cc_start: 0.8712 (p) cc_final: 0.8459 (p) REVERT: H 72 ASP cc_start: 0.6716 (t0) cc_final: 0.6208 (t0) REVERT: H 75 GLU cc_start: 0.7709 (mp0) cc_final: 0.7249 (mp0) REVERT: L 21 ILE cc_start: 0.8200 (mm) cc_final: 0.7979 (tp) REVERT: J 28 THR cc_start: 0.8754 (OUTLIER) cc_final: 0.8356 (p) REVERT: M 50 ASP cc_start: 0.8420 (t70) cc_final: 0.7890 (t0) REVERT: M 74 THR cc_start: 0.8163 (m) cc_final: 0.7462 (p) REVERT: M 91 TYR cc_start: 0.9187 (t80) cc_final: 0.8961 (t80) REVERT: O 72 ASP cc_start: 0.7078 (t0) cc_final: 0.6487 (t0) REVERT: O 75 GLU cc_start: 0.7981 (mp0) cc_final: 0.7685 (mp0) REVERT: Q 21 ILE cc_start: 0.8244 (mm) cc_final: 0.7978 (tp) REVERT: Q 78 LEU cc_start: 0.8454 (tt) cc_final: 0.7872 (tt) REVERT: F 125 LEU cc_start: 0.9335 (mt) cc_final: 0.9065 (tp) REVERT: F 434 MET cc_start: 0.8801 (ttt) cc_final: 0.8344 (ttt) REVERT: K 28 THR cc_start: 0.8817 (OUTLIER) cc_final: 0.8383 (p) REVERT: K 72 ASP cc_start: 0.8010 (t0) cc_final: 0.7574 (t0) REVERT: N 50 ASP cc_start: 0.8405 (t70) cc_final: 0.8138 (t0) REVERT: P 46 GLU cc_start: 0.8101 (tt0) cc_final: 0.7633 (tt0) REVERT: P 72 ASP cc_start: 0.6950 (t0) cc_final: 0.6487 (t0) REVERT: P 75 GLU cc_start: 0.7829 (mp0) cc_final: 0.7168 (mp0) outliers start: 72 outliers final: 48 residues processed: 300 average time/residue: 0.3207 time to fit residues: 158.3973 Evaluate side-chains 281 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 231 time to evaluate : 2.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 81 ASP Chi-restraints excluded: chain G residue 612 SER Chi-restraints excluded: chain G residue 647 GLU Chi-restraints excluded: chain Q residue 17 ASP Chi-restraints excluded: chain Q residue 23 CYS Chi-restraints excluded: chain Q residue 92 ASP Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain K residue 3 GLN Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 52 ASP Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 52 THR Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain I residue 612 SER Chi-restraints excluded: chain I residue 616 ASN Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain R residue 17 ASP Chi-restraints excluded: chain R residue 94 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 239 optimal weight: 0.7980 chunk 162 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 213 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 244 optimal weight: 3.9990 chunk 198 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 146 optimal weight: 0.7980 chunk 257 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 GLN P 39 GLN R 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 25059 Z= 0.204 Angle : 0.537 13.339 34026 Z= 0.278 Chirality : 0.044 0.283 3975 Planarity : 0.003 0.032 4239 Dihedral : 7.792 68.503 4676 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.79 % Allowed : 9.15 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.33 (0.15), residues: 2973 helix: 2.12 (0.29), residues: 390 sheet: 0.47 (0.17), residues: 927 loop : -0.35 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 479 HIS 0.004 0.001 HIS E 374 PHE 0.024 0.002 PHE A 320 TYR 0.022 0.001 TYR Q 49 ARG 0.004 0.000 ARG K 66 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 250 time to evaluate : 2.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 72 ASP cc_start: 0.8008 (t0) cc_final: 0.7663 (t0) REVERT: D 95 THR cc_start: 0.8699 (OUTLIER) cc_final: 0.8417 (p) REVERT: H 72 ASP cc_start: 0.6633 (t0) cc_final: 0.6224 (t0) REVERT: H 75 GLU cc_start: 0.7795 (mp0) cc_final: 0.7313 (mp0) REVERT: L 21 ILE cc_start: 0.8277 (mm) cc_final: 0.8066 (tp) REVERT: L 61 ARG cc_start: 0.8563 (mtm-85) cc_final: 0.8333 (mtm110) REVERT: J 28 THR cc_start: 0.8658 (OUTLIER) cc_final: 0.8238 (p) REVERT: M 50 ASP cc_start: 0.8377 (t70) cc_final: 0.7848 (t0) REVERT: M 74 THR cc_start: 0.8130 (m) cc_final: 0.7404 (p) REVERT: M 91 TYR cc_start: 0.9110 (t80) cc_final: 0.8831 (t80) REVERT: O 72 ASP cc_start: 0.6999 (t0) cc_final: 0.6507 (t0) REVERT: O 75 GLU cc_start: 0.7992 (mp0) cc_final: 0.7710 (mp0) REVERT: Q 21 ILE cc_start: 0.8298 (mm) cc_final: 0.8045 (tp) REVERT: Q 71 TYR cc_start: 0.8256 (m-80) cc_final: 0.7944 (m-80) REVERT: F 125 LEU cc_start: 0.9249 (mt) cc_final: 0.9009 (tp) REVERT: F 426 MET cc_start: 0.8480 (mmm) cc_final: 0.8201 (mtp) REVERT: F 434 MET cc_start: 0.8753 (ttt) cc_final: 0.8277 (ttt) REVERT: K 28 THR cc_start: 0.8781 (OUTLIER) cc_final: 0.8316 (p) REVERT: K 72 ASP cc_start: 0.7952 (t0) cc_final: 0.7568 (t0) REVERT: K 94 THR cc_start: 0.8944 (OUTLIER) cc_final: 0.8666 (t) REVERT: K 97 MET cc_start: 0.8576 (ttm) cc_final: 0.8283 (ttm) REVERT: N 50 ASP cc_start: 0.8348 (t70) cc_final: 0.8059 (t0) REVERT: P 46 GLU cc_start: 0.7989 (tt0) cc_final: 0.7519 (tt0) REVERT: P 72 ASP cc_start: 0.6930 (t0) cc_final: 0.6539 (t0) REVERT: P 75 GLU cc_start: 0.7881 (mp0) cc_final: 0.7255 (mp0) REVERT: R 78 LEU cc_start: 0.8410 (tt) cc_final: 0.8129 (tt) outliers start: 47 outliers final: 33 residues processed: 287 average time/residue: 0.3199 time to fit residues: 151.0193 Evaluate side-chains 273 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 236 time to evaluate : 2.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain L residue 17 ASP Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 81 ASP Chi-restraints excluded: chain G residue 612 SER Chi-restraints excluded: chain Q residue 23 CYS Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 52 ASP Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 52 THR Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain R residue 94 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 96 optimal weight: 10.0000 chunk 258 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 168 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 287 optimal weight: 3.9990 chunk 238 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 150 optimal weight: 4.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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** D 79 GLN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 25059 Z= 0.397 Angle : 0.618 14.120 34026 Z= 0.318 Chirality : 0.046 0.278 3975 Planarity : 0.004 0.035 4239 Dihedral : 7.919 68.547 4674 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.87 % Allowed : 10.03 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.14 (0.15), residues: 2973 helix: 1.93 (0.28), residues: 390 sheet: 0.38 (0.17), residues: 897 loop : -0.48 (0.14), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP J 103 HIS 0.007 0.001 HIS F 330 PHE 0.030 0.002 PHE E 320 TYR 0.024 0.002 TYR L 49 ARG 0.006 0.000 ARG K 66 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 237 time to evaluate : 3.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 72 ASP cc_start: 0.8097 (t0) cc_final: 0.7754 (t0) REVERT: D 95 THR cc_start: 0.8708 (p) cc_final: 0.8436 (p) REVERT: H 72 ASP cc_start: 0.6689 (t0) cc_final: 0.6221 (t0) REVERT: H 75 GLU cc_start: 0.7802 (mp0) cc_final: 0.7344 (mp0) REVERT: L 21 ILE cc_start: 0.8321 (mm) cc_final: 0.8091 (tp) REVERT: J 28 THR cc_start: 0.8675 (OUTLIER) cc_final: 0.8260 (p) REVERT: M 50 ASP cc_start: 0.8311 (t70) cc_final: 0.7771 (t0) REVERT: M 74 THR cc_start: 0.8228 (m) cc_final: 0.7536 (p) REVERT: M 91 TYR cc_start: 0.9177 (t80) cc_final: 0.8896 (t80) REVERT: O 72 ASP cc_start: 0.7055 (t0) cc_final: 0.6563 (t0) REVERT: O 75 GLU cc_start: 0.8042 (mp0) cc_final: 0.7748 (mp0) REVERT: Q 21 ILE cc_start: 0.8291 (mm) cc_final: 0.8021 (tp) REVERT: F 125 LEU cc_start: 0.9354 (mt) cc_final: 0.9083 (tp) REVERT: F 426 MET cc_start: 0.8557 (mmm) cc_final: 0.8243 (mtp) REVERT: F 434 MET cc_start: 0.8760 (ttt) cc_final: 0.8354 (ttt) REVERT: K 28 THR cc_start: 0.8800 (OUTLIER) cc_final: 0.8365 (p) REVERT: K 72 ASP cc_start: 0.8011 (t0) cc_final: 0.7615 (t0) REVERT: K 97 MET cc_start: 0.8705 (ttm) cc_final: 0.8391 (ttm) REVERT: N 50 ASP cc_start: 0.8364 (t70) cc_final: 0.8098 (t0) REVERT: P 46 GLU cc_start: 0.7997 (tt0) cc_final: 0.7548 (tt0) REVERT: P 72 ASP cc_start: 0.6967 (t0) cc_final: 0.6566 (t0) REVERT: P 75 GLU cc_start: 0.7914 (mp0) cc_final: 0.7252 (mp0) outliers start: 49 outliers final: 42 residues processed: 276 average time/residue: 0.3246 time to fit residues: 147.3392 Evaluate side-chains 271 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 227 time to evaluate : 2.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 621 GLU Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain L residue 17 ASP Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 81 ASP Chi-restraints excluded: chain G residue 612 SER Chi-restraints excluded: chain G residue 616 ASN Chi-restraints excluded: chain Q residue 17 ASP Chi-restraints excluded: chain Q residue 23 CYS Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 52 ASP Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 52 THR Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 81 ASP Chi-restraints excluded: chain I residue 612 SER Chi-restraints excluded: chain I residue 616 ASN Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain R residue 17 ASP Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 104 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 277 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 163 optimal weight: 0.4980 chunk 209 optimal weight: 2.9990 chunk 162 optimal weight: 0.7980 chunk 241 optimal weight: 6.9990 chunk 160 optimal weight: 8.9990 chunk 286 optimal weight: 2.9990 chunk 179 optimal weight: 0.4980 chunk 174 optimal weight: 0.5980 chunk 132 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 17 GLN N 79 GLN P 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 25059 Z= 0.174 Angle : 0.531 13.619 34026 Z= 0.273 Chirality : 0.043 0.261 3975 Planarity : 0.003 0.035 4239 Dihedral : 7.444 64.485 4674 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.72 % Allowed : 10.64 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.33 (0.15), residues: 2973 helix: 2.27 (0.29), residues: 390 sheet: 0.48 (0.18), residues: 891 loop : -0.39 (0.15), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 479 HIS 0.004 0.001 HIS E 374 PHE 0.024 0.001 PHE A 320 TYR 0.023 0.001 TYR L 49 ARG 0.004 0.000 ARG B 617 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 254 time to evaluate : 2.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 72 ASP cc_start: 0.7991 (t0) cc_final: 0.7642 (t0) REVERT: D 95 THR cc_start: 0.8681 (p) cc_final: 0.8398 (p) REVERT: H 72 ASP cc_start: 0.6664 (t0) cc_final: 0.6219 (t0) REVERT: H 75 GLU cc_start: 0.7856 (mp0) cc_final: 0.7398 (mp0) REVERT: L 21 ILE cc_start: 0.8270 (mm) cc_final: 0.8008 (tp) REVERT: J 28 THR cc_start: 0.8580 (OUTLIER) cc_final: 0.8163 (p) REVERT: M 50 ASP cc_start: 0.8200 (t70) cc_final: 0.7662 (t0) REVERT: M 74 THR cc_start: 0.8198 (m) cc_final: 0.7506 (p) REVERT: M 91 TYR cc_start: 0.9099 (t80) cc_final: 0.8803 (t80) REVERT: O 72 ASP cc_start: 0.7022 (t0) cc_final: 0.6541 (t0) REVERT: O 75 GLU cc_start: 0.8011 (mp0) cc_final: 0.7701 (mp0) REVERT: Q 21 ILE cc_start: 0.8289 (mm) cc_final: 0.8070 (tp) REVERT: Q 61 ARG cc_start: 0.8471 (mtm-85) cc_final: 0.7853 (mtm180) REVERT: Q 71 TYR cc_start: 0.8166 (m-80) cc_final: 0.7700 (m-10) REVERT: F 161 MET cc_start: 0.8509 (tpt) cc_final: 0.7954 (tpt) REVERT: F 426 MET cc_start: 0.8478 (mmm) cc_final: 0.8164 (mtp) REVERT: F 434 MET cc_start: 0.8733 (ttt) cc_final: 0.8264 (ttt) REVERT: K 28 THR cc_start: 0.8677 (OUTLIER) cc_final: 0.8199 (p) REVERT: K 72 ASP cc_start: 0.7927 (t0) cc_final: 0.7569 (t0) REVERT: K 97 MET cc_start: 0.8611 (ttm) cc_final: 0.8355 (ttm) REVERT: N 50 ASP cc_start: 0.8303 (t70) cc_final: 0.8021 (t0) REVERT: P 46 GLU cc_start: 0.7916 (tt0) cc_final: 0.7494 (tt0) REVERT: P 72 ASP cc_start: 0.6951 (t0) cc_final: 0.6622 (t0) REVERT: P 75 GLU cc_start: 0.7926 (mp0) cc_final: 0.7279 (mp0) REVERT: R 78 LEU cc_start: 0.8346 (tt) cc_final: 0.8099 (tt) outliers start: 45 outliers final: 25 residues processed: 288 average time/residue: 0.3384 time to fit residues: 158.5868 Evaluate side-chains 262 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 235 time to evaluate : 3.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 81 ASP Chi-restraints excluded: chain G residue 612 SER Chi-restraints excluded: chain Q residue 23 CYS Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 52 ASP Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 52 THR Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain I residue 612 SER Chi-restraints excluded: chain P residue 12 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 177 optimal weight: 7.9990 chunk 114 optimal weight: 1.9990 chunk 170 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 55 optimal weight: 0.5980 chunk 181 optimal weight: 3.9990 chunk 195 optimal weight: 10.0000 chunk 141 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 225 optimal weight: 3.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- 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** H 3 GLN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 53 GLN G 585 HIS ** O 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 25059 Z= 0.409 Angle : 0.626 13.602 34026 Z= 0.321 Chirality : 0.046 0.267 3975 Planarity : 0.004 0.038 4239 Dihedral : 7.692 64.524 4674 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.64 % Allowed : 11.48 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.06 (0.15), residues: 2973 helix: 2.01 (0.28), residues: 387 sheet: 0.35 (0.17), residues: 900 loop : -0.59 (0.14), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 103 HIS 0.008 0.001 HIS E 330 PHE 0.029 0.002 PHE A 320 TYR 0.025 0.002 TYR D 91 ARG 0.005 0.001 ARG F 139 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 236 time to evaluate : 2.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 72 ASP cc_start: 0.8112 (t0) cc_final: 0.7774 (t0) REVERT: D 95 THR cc_start: 0.8710 (p) cc_final: 0.8435 (p) REVERT: H 72 ASP cc_start: 0.6745 (t0) cc_final: 0.6326 (t0) REVERT: H 75 GLU cc_start: 0.7896 (mp0) cc_final: 0.7455 (mp0) REVERT: L 21 ILE cc_start: 0.8273 (mm) cc_final: 0.7959 (tp) REVERT: J 28 THR cc_start: 0.8554 (OUTLIER) cc_final: 0.8054 (p) REVERT: J 72 ASP cc_start: 0.8099 (t0) cc_final: 0.7758 (t0) REVERT: M 50 ASP cc_start: 0.8182 (t70) cc_final: 0.7661 (t0) REVERT: M 74 THR cc_start: 0.8259 (m) cc_final: 0.7575 (p) REVERT: M 91 TYR cc_start: 0.9188 (t80) cc_final: 0.8882 (t80) REVERT: O 72 ASP cc_start: 0.7082 (t0) cc_final: 0.6604 (t0) REVERT: O 75 GLU cc_start: 0.8082 (mp0) cc_final: 0.7753 (mp0) REVERT: Q 21 ILE cc_start: 0.8258 (mm) cc_final: 0.8003 (tp) REVERT: Q 71 TYR cc_start: 0.8105 (m-80) cc_final: 0.7704 (m-80) REVERT: F 434 MET cc_start: 0.8728 (ttt) cc_final: 0.8306 (ttt) REVERT: K 28 THR cc_start: 0.8692 (p) cc_final: 0.8163 (p) REVERT: K 72 ASP cc_start: 0.8003 (t0) cc_final: 0.7625 (t0) REVERT: K 97 MET cc_start: 0.8668 (ttm) cc_final: 0.8398 (ttm) REVERT: N 50 ASP cc_start: 0.8361 (t70) cc_final: 0.8088 (t0) REVERT: P 46 GLU cc_start: 0.7994 (tt0) cc_final: 0.7566 (tt0) REVERT: P 72 ASP cc_start: 0.7060 (t0) cc_final: 0.6687 (t0) REVERT: P 75 GLU cc_start: 0.7980 (mp0) cc_final: 0.7296 (mp0) REVERT: R 3 GLN cc_start: 0.7802 (mm-40) cc_final: 0.7506 (mm-40) REVERT: R 78 LEU cc_start: 0.8375 (tt) cc_final: 0.8093 (tt) outliers start: 43 outliers final: 33 residues processed: 266 average time/residue: 0.3161 time to fit residues: 137.6699 Evaluate side-chains 264 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 230 time to evaluate : 2.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 53 GLN Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 81 ASP Chi-restraints excluded: chain G residue 612 SER Chi-restraints excluded: chain Q residue 17 ASP Chi-restraints excluded: chain Q residue 23 CYS Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain K residue 52 ASP Chi-restraints excluded: chain K residue 101 ASP Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 52 THR Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain I residue 612 SER Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain R residue 104 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 260 optimal weight: 8.9990 chunk 274 optimal weight: 1.9990 chunk 250 optimal weight: 4.9990 chunk 266 optimal weight: 1.9990 chunk 160 optimal weight: 7.9990 chunk 116 optimal weight: 0.9980 chunk 209 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 241 optimal weight: 0.0050 chunk 252 optimal weight: 0.9980 chunk 265 optimal weight: 0.8980 overall best weight: 0.9796 ------------------------------------------------------------------------------- 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** H 3 GLN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 585 HIS ** O 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN P 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 25059 Z= 0.226 Angle : 0.560 13.021 34026 Z= 0.287 Chirality : 0.044 0.254 3975 Planarity : 0.003 0.038 4239 Dihedral : 7.453 61.903 4674 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.33 % Allowed : 11.98 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.15 (0.15), residues: 2973 helix: 2.21 (0.29), residues: 387 sheet: 0.39 (0.18), residues: 879 loop : -0.54 (0.14), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 479 HIS 0.004 0.001 HIS E 330 PHE 0.022 0.002 PHE A 320 TYR 0.023 0.001 TYR L 49 ARG 0.006 0.000 ARG M 54 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 239 time to evaluate : 2.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 72 ASP cc_start: 0.8053 (t0) cc_final: 0.7718 (t0) REVERT: D 95 THR cc_start: 0.8692 (p) cc_final: 0.8407 (p) REVERT: H 72 ASP cc_start: 0.6740 (t0) cc_final: 0.6324 (t0) REVERT: H 75 GLU cc_start: 0.7920 (mp0) cc_final: 0.7499 (mp0) REVERT: L 21 ILE cc_start: 0.8231 (mm) cc_final: 0.7969 (tp) REVERT: J 28 THR cc_start: 0.8520 (OUTLIER) cc_final: 0.8008 (p) REVERT: J 72 ASP cc_start: 0.8077 (t0) cc_final: 0.7748 (t0) REVERT: M 50 ASP cc_start: 0.8129 (t70) cc_final: 0.7742 (t0) REVERT: M 74 THR cc_start: 0.8245 (m) cc_final: 0.7556 (p) REVERT: M 91 TYR cc_start: 0.9145 (t80) cc_final: 0.8851 (t80) REVERT: O 72 ASP cc_start: 0.6993 (t0) cc_final: 0.6548 (t0) REVERT: O 75 GLU cc_start: 0.8066 (mp0) cc_final: 0.7741 (mp0) REVERT: Q 21 ILE cc_start: 0.8285 (mm) cc_final: 0.8059 (tp) REVERT: Q 71 TYR cc_start: 0.8060 (m-80) cc_final: 0.7574 (m-10) REVERT: F 161 MET cc_start: 0.8534 (tpt) cc_final: 0.7983 (tpt) REVERT: F 426 MET cc_start: 0.8418 (mmm) cc_final: 0.8183 (mtp) REVERT: F 434 MET cc_start: 0.8718 (ttt) cc_final: 0.8310 (ttt) REVERT: K 28 THR cc_start: 0.8627 (OUTLIER) cc_final: 0.8084 (p) REVERT: K 72 ASP cc_start: 0.7946 (t0) cc_final: 0.7574 (t0) REVERT: K 97 MET cc_start: 0.8643 (ttm) cc_final: 0.8366 (ttm) REVERT: N 50 ASP cc_start: 0.8315 (t70) cc_final: 0.8040 (t0) REVERT: P 46 GLU cc_start: 0.7991 (tt0) cc_final: 0.7545 (tt0) REVERT: P 72 ASP cc_start: 0.7051 (t0) cc_final: 0.6711 (t0) REVERT: P 75 GLU cc_start: 0.7932 (mp0) cc_final: 0.7230 (mp0) REVERT: R 78 LEU cc_start: 0.8372 (tt) cc_final: 0.8091 (tt) outliers start: 35 outliers final: 29 residues processed: 265 average time/residue: 0.3295 time to fit residues: 142.8202 Evaluate side-chains 263 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 232 time to evaluate : 2.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain L residue 17 ASP Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 81 ASP Chi-restraints excluded: chain G residue 612 SER Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain Q residue 17 ASP Chi-restraints excluded: chain Q residue 23 CYS Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 241 ASN Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 52 ASP Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 52 THR Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain I residue 612 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 175 optimal weight: 3.9990 chunk 282 optimal weight: 5.9990 chunk 172 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 196 optimal weight: 0.9990 chunk 295 optimal weight: 1.9990 chunk 272 optimal weight: 1.9990 chunk 235 optimal weight: 0.3980 chunk 24 optimal weight: 1.9990 chunk 181 optimal weight: 0.5980 chunk 144 optimal weight: 3.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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** H 3 GLN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 53 GLN G 585 HIS ** O 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 25059 Z= 0.264 Angle : 0.561 12.497 34026 Z= 0.287 Chirality : 0.044 0.253 3975 Planarity : 0.003 0.040 4239 Dihedral : 7.299 59.731 4674 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.22 % Allowed : 12.20 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.15), residues: 2973 helix: 2.23 (0.29), residues: 387 sheet: 0.38 (0.18), residues: 879 loop : -0.56 (0.14), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 36 HIS 0.005 0.001 HIS E 330 PHE 0.022 0.002 PHE A 320 TYR 0.026 0.001 TYR D 91 ARG 0.003 0.000 ARG K 66 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 236 time to evaluate : 2.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 72 ASP cc_start: 0.8073 (t0) cc_final: 0.7737 (t0) REVERT: D 95 THR cc_start: 0.8683 (p) cc_final: 0.8403 (p) REVERT: B 621 GLU cc_start: 0.7744 (tm-30) cc_final: 0.7210 (tm-30) REVERT: H 72 ASP cc_start: 0.6683 (t0) cc_final: 0.6228 (t0) REVERT: H 75 GLU cc_start: 0.7883 (mp0) cc_final: 0.7441 (mp0) REVERT: L 21 ILE cc_start: 0.8292 (mm) cc_final: 0.8047 (tp) REVERT: J 28 THR cc_start: 0.8472 (p) cc_final: 0.7940 (p) REVERT: J 72 ASP cc_start: 0.8089 (t0) cc_final: 0.7815 (t0) REVERT: M 50 ASP cc_start: 0.8204 (t70) cc_final: 0.7662 (t0) REVERT: M 74 THR cc_start: 0.8269 (m) cc_final: 0.7582 (p) REVERT: M 91 TYR cc_start: 0.9154 (t80) cc_final: 0.8854 (t80) REVERT: O 72 ASP cc_start: 0.7003 (t0) cc_final: 0.6535 (t0) REVERT: O 75 GLU cc_start: 0.8118 (mp0) cc_final: 0.7761 (mp0) REVERT: Q 71 TYR cc_start: 0.8041 (m-80) cc_final: 0.7555 (m-10) REVERT: F 161 MET cc_start: 0.8532 (tpt) cc_final: 0.7994 (tpt) REVERT: F 426 MET cc_start: 0.8446 (mmm) cc_final: 0.8205 (mtp) REVERT: F 434 MET cc_start: 0.8721 (ttt) cc_final: 0.8298 (ttt) REVERT: K 28 THR cc_start: 0.8557 (OUTLIER) cc_final: 0.7974 (p) REVERT: K 72 ASP cc_start: 0.7976 (t0) cc_final: 0.7604 (t0) REVERT: K 97 MET cc_start: 0.8631 (ttm) cc_final: 0.8348 (ttm) REVERT: N 50 ASP cc_start: 0.8326 (t70) cc_final: 0.8052 (t0) REVERT: P 46 GLU cc_start: 0.7977 (tt0) cc_final: 0.7545 (tt0) REVERT: P 72 ASP cc_start: 0.7085 (t0) cc_final: 0.6764 (t0) REVERT: P 75 GLU cc_start: 0.7966 (mp0) cc_final: 0.7298 (mp0) REVERT: R 78 LEU cc_start: 0.8362 (tt) cc_final: 0.8099 (tt) outliers start: 32 outliers final: 28 residues processed: 261 average time/residue: 0.3289 time to fit residues: 139.8818 Evaluate side-chains 260 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 231 time to evaluate : 2.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 81 ASP Chi-restraints excluded: chain G residue 612 SER Chi-restraints excluded: chain Q residue 17 ASP Chi-restraints excluded: chain Q residue 23 CYS Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 241 ASN Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 52 ASP Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 52 THR Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain I residue 612 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 187 optimal weight: 0.9980 chunk 250 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 217 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 65 optimal weight: 0.4980 chunk 235 optimal weight: 0.4980 chunk 98 optimal weight: 0.9990 chunk 242 optimal weight: 3.9990 chunk 29 optimal weight: 0.0470 chunk 43 optimal weight: 6.9990 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 82AHIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.085587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.066780 restraints weight = 54642.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.068951 restraints weight = 31543.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.070370 restraints weight = 22101.352| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 25059 Z= 0.174 Angle : 0.532 11.676 34026 Z= 0.273 Chirality : 0.043 0.252 3975 Planarity : 0.003 0.039 4239 Dihedral : 6.968 59.504 4674 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.14 % Allowed : 12.40 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.31 (0.16), residues: 2973 helix: 2.36 (0.29), residues: 390 sheet: 0.63 (0.18), residues: 843 loop : -0.51 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 34 HIS 0.003 0.001 HIS E 374 PHE 0.019 0.001 PHE A 320 TYR 0.023 0.001 TYR L 49 ARG 0.003 0.000 ARG K 66 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4367.89 seconds wall clock time: 80 minutes 1.73 seconds (4801.73 seconds total)