Starting phenix.real_space_refine on Mon Sep 30 07:27:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t49_41024/09_2024/8t49_41024.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t49_41024/09_2024/8t49_41024.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t49_41024/09_2024/8t49_41024.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t49_41024/09_2024/8t49_41024.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t49_41024/09_2024/8t49_41024.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t49_41024/09_2024/8t49_41024.cif" } resolution = 3.2 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= 0.036 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 144 5.16 5 C 15642 2.51 5 N 4140 2.21 5 O 5013 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 24939 Number of models: 1 Model: "" Number of chains: 12 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: "H" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 967 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "L" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 798 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} 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: "S" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" 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: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Restraints were copied for chains: G, I, O, P, W, a, K, J, Z, d, Y, c, M, N, E, F, X, b, Q, R Time building chain proxies: 14.77, per 1000 atoms: 0.59 Number of scatterers: 24939 At special positions: 0 Unit cell: (146.05, 149.5, 172.5, 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 144 16.00 O 5013 8.00 N 4140 7.00 C 15642 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, 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=2.03 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=2.02 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 C 22 " - pdb=" SG CYS C 92 " distance=2.04 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 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 ALPHA1-2 " MAN S 4 " - " MAN S 5 " " MAN W 4 " - " MAN W 5 " " MAN a 4 " - " MAN a 5 " ALPHA1-3 " BMA S 3 " - " MAN S 4 " " BMA U 3 " - " MAN U 4 " " BMA W 3 " - " MAN W 4 " " BMA Y 3 " - " MAN Y 4 " " BMA a 3 " - " MAN a 4 " " BMA c 3 " - " MAN c 4 " ALPHA1-6 " BMA S 3 " - " MAN S 6 " " BMA W 3 " - " MAN W 6 " " BMA a 3 " - " MAN a 6 " BETA1-4 " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " 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 Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " NAG-ASN " NAG A 601 " - " ASN A 301 " " NAG A 602 " - " ASN A 88 " " NAG A 603 " - " ASN A 160 " " NAG A 604 " - " ASN A 197 " " NAG A 605 " - " ASN A 234 " " NAG A 606 " - " ASN A 276 " " NAG A 607 " - " ASN A 295 " " NAG A 608 " - " ASN A 339 " " NAG A 609 " - " ASN A 386 " " NAG A 610 " - " ASN A 448 " " NAG A 611 " - " ASN A 289 " " NAG A 612 " - " ASN A 241 " " NAG A 613 " - " ASN A 355 " " NAG A 614 " - " ASN A 392 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 637 " " NAG E 601 " - " ASN E 301 " " NAG E 602 " - " ASN E 88 " " NAG E 603 " - " ASN E 160 " " NAG E 604 " - " ASN E 197 " " NAG E 605 " - " ASN E 234 " " NAG E 606 " - " ASN E 276 " " NAG E 607 " - " ASN E 295 " " NAG E 608 " - " ASN E 339 " " NAG E 609 " - " ASN E 386 " " NAG E 610 " - " ASN E 448 " " NAG E 611 " - " ASN E 289 " " NAG E 612 " - " ASN E 241 " " NAG E 613 " - " ASN E 355 " " NAG E 614 " - " ASN E 392 " " NAG F 601 " - " ASN F 301 " " NAG F 602 " - " ASN F 88 " " NAG F 603 " - " ASN F 160 " " NAG F 604 " - " ASN F 197 " " NAG F 605 " - " ASN F 234 " " NAG F 606 " - " ASN F 276 " " NAG F 607 " - " ASN F 295 " " NAG F 608 " - " ASN F 339 " " NAG F 609 " - " ASN F 386 " " NAG F 610 " - " ASN F 448 " " NAG F 611 " - " ASN F 289 " " NAG F 612 " - " ASN F 241 " " NAG F 613 " - " ASN F 355 " " NAG F 614 " - " ASN F 392 " " NAG G 701 " - " ASN G 611 " " NAG G 702 " - " ASN G 618 " " NAG G 703 " - " ASN G 637 " " NAG I 701 " - " ASN I 611 " " NAG I 702 " - " ASN I 618 " " NAG I 703 " - " ASN I 637 " " NAG S 1 " - " ASN A 332 " " NAG T 1 " - " ASN A 156 " " NAG U 1 " - " ASN A 262 " " NAG V 1 " - " ASN H 60 " " NAG W 1 " - " ASN E 332 " " NAG X 1 " - " ASN E 156 " " NAG Y 1 " - " ASN E 262 " " NAG Z 1 " - " ASN O 60 " " NAG a 1 " - " ASN F 332 " " NAG b 1 " - " ASN F 156 " " NAG c 1 " - " ASN F 262 " " NAG d 1 " - " ASN P 60 " Time building additional restraints: 7.36 Conformation dependent library (CDL) restraints added in 3.0 seconds 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 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: 78 helices and 45 sheets defined 20.7% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.44 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 195 through 198 Processing helix chain 'A' and resid 335 through 354 removed outlier: 4.030A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 425 through 429 removed outlier: 4.247A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 484 removed outlier: 4.227A pdb=" N ASN A 478 " --> pdb=" O ASP A 474 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 65 No H-bonds generated for 'chain 'H' and resid 63 through 65' Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 100B through 100F Processing helix chain 'L' and resid 26 through 30 removed outlier: 3.652A pdb=" N GLU L 29 " --> pdb=" O ASP L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 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: 4.085A pdb=" N GLU D 83 " --> pdb=" O ALA D 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.441A 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 543 removed outlier: 3.585A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 596 Processing helix chain 'B' and resid 618 through 626 removed outlier: 3.667A pdb=" N MET B 626 " --> pdb=" O ILE B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 662 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 195 through 198 Processing helix chain 'E' and resid 335 through 354 removed outlier: 4.030A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 391 Processing helix chain 'E' and resid 425 through 429 removed outlier: 4.247A pdb=" N GLN E 428 " --> pdb=" O ASN E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 474 through 484 removed outlier: 4.227A pdb=" N ASN E 478 " --> pdb=" O ASP E 474 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'O' and resid 63 through 65 No H-bonds generated for 'chain 'O' and resid 63 through 65' Processing helix chain 'O' and resid 73 through 75 No H-bonds generated for 'chain 'O' and resid 73 through 75' Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'O' and resid 100B through 100F Processing helix chain 'Q' and resid 26 through 30 removed outlier: 3.652A pdb=" N GLU Q 29 " --> pdb=" O ASP Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 83 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: 4.084A pdb=" N GLU M 83 " --> pdb=" O ALA M 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 523 through 528 removed outlier: 4.441A 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 543 removed outlier: 3.585A pdb=" N GLN G 540 " --> pdb=" O THR G 536 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN G 543 " --> pdb=" O VAL G 539 " (cutoff:3.500A) Processing helix chain 'G' and resid 573 through 596 Processing helix chain 'G' and resid 618 through 626 removed outlier: 3.668A pdb=" N MET G 626 " --> pdb=" O ILE G 622 " (cutoff:3.500A) Processing helix chain 'G' and resid 627 through 635 Processing helix chain 'G' and resid 638 through 662 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 195 through 198 Processing helix chain 'F' and resid 335 through 354 removed outlier: 4.030A pdb=" N HIS F 352 " --> pdb=" O GLN F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 387 through 391 Processing helix chain 'F' and resid 425 through 429 removed outlier: 4.247A pdb=" N GLN F 428 " --> pdb=" O ASN F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 474 through 484 removed outlier: 4.227A pdb=" N ASN F 478 " --> pdb=" O ASP F 474 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU F 482 " --> pdb=" O ASN F 478 " (cutoff:3.500A) Processing helix chain 'P' and resid 63 through 65 No H-bonds generated for 'chain 'P' and resid 63 through 65' Processing helix chain 'P' and resid 73 through 75 No H-bonds generated for 'chain 'P' and resid 73 through 75' Processing helix chain 'P' and resid 83 through 87 Processing helix chain 'P' and resid 100B through 100F Processing helix chain 'R' and resid 26 through 30 removed outlier: 3.652A pdb=" N GLU R 29 " --> pdb=" O ASP R 26 " (cutoff:3.500A) Processing helix chain 'R' and resid 79 through 83 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: 4.085A pdb=" N GLU N 83 " --> pdb=" O ALA N 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 523 through 528 removed outlier: 4.441A 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 543 removed outlier: 3.585A pdb=" N GLN I 540 " --> pdb=" O THR I 536 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN I 543 " --> pdb=" O VAL I 539 " (cutoff:3.500A) Processing helix chain 'I' and resid 573 through 596 Processing helix chain 'I' and resid 618 through 626 removed outlier: 3.667A pdb=" N MET I 626 " --> pdb=" O ILE I 622 " (cutoff:3.500A) Processing helix chain 'I' and resid 627 through 635 Processing helix chain 'I' and resid 638 through 662 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.360A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.061A 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 Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 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: 6.446A 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: 7.059A pdb=" N ASN A 301 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N VAL A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.276A 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 'H' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'H' and resid 34 through 39 removed outlier: 6.762A pdb=" N TRP H 35 " --> pdb=" O ASN H 50 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ASN H 50 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 6.571A 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 100H through 103 Processing sheet with id=AB1, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AB2, first strand: chain 'L' and resid 9 through 12 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 9 through 12 current: chain 'L' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 45 through 48 current: chain 'L' and resid 97 through 98 No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.807A pdb=" N GLY C 16 " --> pdb=" O SER C 82B" (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 34 through 39 removed outlier: 5.805A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.290A 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=AB5, first strand: chain 'D' and resid 19 through 24 Processing sheet with id=AB6, first strand: chain 'D' and resid 33 through 38 removed outlier: 6.268A 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=AB7, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.361A pdb=" N VAL G 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N VAL E 38 " --> pdb=" O THR G 606 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N THR G 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N TYR E 40 " --> pdb=" O CYS G 604 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N CYS G 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AB9, first strand: chain 'E' and resid 75 through 76 Processing sheet with id=AC1, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AC2, first strand: chain 'E' and resid 172 through 177 Processing sheet with id=AC3, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.446A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AC4, 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: 7.059A pdb=" N ASN E 301 " --> pdb=" O VAL E 323 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N VAL E 323 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 6.276A 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=AC5, first strand: chain 'O' and resid 3 through 7 Processing sheet with id=AC6, first strand: chain 'O' and resid 34 through 39 removed outlier: 6.762A pdb=" N TRP O 35 " --> pdb=" O ASN O 50 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ASN O 50 " --> pdb=" O TRP O 35 " (cutoff:3.500A) removed outlier: 6.572A 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 100H through 103 Processing sheet with id=AC7, first strand: chain 'Q' and resid 5 through 6 Processing sheet with id=AC8, first strand: chain 'Q' and resid 9 through 12 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 9 through 12 current: chain 'Q' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 45 through 48 current: chain 'Q' and resid 97 through 98 No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'J' and resid 3 through 7 removed outlier: 3.807A pdb=" N GLY J 16 " --> pdb=" O SER J 82B" (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 34 through 39 removed outlier: 5.804A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.290A 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=AD2, first strand: chain 'M' and resid 19 through 24 Processing sheet with id=AD3, first strand: chain 'M' and resid 33 through 38 removed outlier: 6.268A 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=AD4, first strand: chain 'F' and resid 494 through 499 removed outlier: 5.360A pdb=" N VAL I 608 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N VAL F 38 " --> pdb=" O THR I 606 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N THR I 606 " --> pdb=" O VAL F 38 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N TYR F 40 " --> pdb=" O CYS I 604 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N CYS I 604 " --> pdb=" O TYR F 40 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 45 through 47 Processing sheet with id=AD6, first strand: chain 'F' and resid 75 through 76 Processing sheet with id=AD7, first strand: chain 'F' and resid 91 through 94 Processing sheet with id=AD8, first strand: chain 'F' and resid 172 through 177 Processing sheet with id=AD9, first strand: chain 'F' and resid 201 through 203 removed outlier: 6.446A pdb=" N THR F 202 " --> pdb=" O TYR F 435 " (cutoff:3.500A) Processing sheet with id=AE1, 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: 7.059A pdb=" N ASN F 301 " --> pdb=" O VAL F 323 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N VAL F 323 " --> pdb=" O ASN F 301 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N THR F 303 " --> pdb=" O GLY F 321 " (cutoff:3.500A) removed outlier: 6.276A 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=AE2, first strand: chain 'P' and resid 3 through 7 Processing sheet with id=AE3, first strand: chain 'P' and resid 34 through 39 removed outlier: 6.762A pdb=" N TRP P 35 " --> pdb=" O ASN P 50 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ASN P 50 " --> pdb=" O TRP P 35 " (cutoff:3.500A) removed outlier: 6.572A 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 100H through 103 Processing sheet with id=AE4, first strand: chain 'R' and resid 5 through 6 Processing sheet with id=AE5, first strand: chain 'R' and resid 9 through 12 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 9 through 12 current: chain 'R' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 45 through 48 current: chain 'R' and resid 97 through 98 No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'K' and resid 3 through 7 removed outlier: 3.808A pdb=" N GLY K 16 " --> pdb=" O SER K 82B" (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 34 through 39 removed outlier: 5.804A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 5.290A 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=AE8, first strand: chain 'N' and resid 19 through 24 Processing sheet with id=AE9, first strand: chain 'N' and resid 33 through 38 removed outlier: 6.268A 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 98 720 hydrogen bonds defined for protein. 1782 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: 7.83 Time building geometry restraints manager: 8.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7833 1.35 - 1.47: 6705 1.47 - 1.60: 10716 1.60 - 1.72: 0 1.72 - 1.85: 198 Bond restraints: 25452 Sorted by residual: bond pdb=" C1 NAG V 2 " pdb=" O5 NAG V 2 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.59e+00 bond pdb=" C5 MAN S 5 " pdb=" O5 MAN S 5 " ideal model delta sigma weight residual 1.418 1.465 -0.047 2.00e-02 2.50e+03 5.57e+00 bond pdb=" C5 MAN W 5 " pdb=" O5 MAN W 5 " ideal model delta sigma weight residual 1.418 1.465 -0.047 2.00e-02 2.50e+03 5.53e+00 bond pdb=" C1 NAG Z 2 " pdb=" O5 NAG Z 2 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.53e+00 bond pdb=" C1 NAG d 2 " pdb=" O5 NAG d 2 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.49e+00 ... (remaining 25447 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 32477 2.23 - 4.47: 1773 4.47 - 6.70: 265 6.70 - 8.93: 27 8.93 - 11.16: 12 Bond angle restraints: 34554 Sorted by residual: angle pdb=" N LEU Q 97 " pdb=" CA LEU Q 97 " pdb=" C LEU Q 97 " ideal model delta sigma weight residual 107.93 96.77 11.16 1.65e+00 3.67e-01 4.58e+01 angle pdb=" N LEU L 97 " pdb=" CA LEU L 97 " pdb=" C LEU L 97 " ideal model delta sigma weight residual 107.93 96.78 11.15 1.65e+00 3.67e-01 4.57e+01 angle pdb=" N LEU R 97 " pdb=" CA LEU R 97 " pdb=" C LEU R 97 " ideal model delta sigma weight residual 107.93 96.79 11.14 1.65e+00 3.67e-01 4.56e+01 angle pdb=" CA TRP H 47 " pdb=" CB TRP H 47 " pdb=" CG TRP H 47 " ideal model delta sigma weight residual 113.60 122.87 -9.27 1.90e+00 2.77e-01 2.38e+01 angle pdb=" CA TRP O 47 " pdb=" CB TRP O 47 " pdb=" CG TRP O 47 " ideal model delta sigma weight residual 113.60 122.87 -9.27 1.90e+00 2.77e-01 2.38e+01 ... (remaining 34549 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.50: 15484 21.50 - 42.99: 513 42.99 - 64.49: 131 64.49 - 85.99: 81 85.99 - 107.49: 39 Dihedral angle restraints: 16248 sinusoidal: 7554 harmonic: 8694 Sorted by residual: dihedral pdb=" CB CYS A 378 " pdb=" SG CYS A 378 " pdb=" SG CYS A 445 " pdb=" CB CYS A 445 " ideal model delta sinusoidal sigma weight residual -86.00 -136.36 50.36 1 1.00e+01 1.00e-02 3.48e+01 dihedral pdb=" CB CYS C 22 " pdb=" SG CYS C 22 " pdb=" SG CYS C 92 " pdb=" CB CYS C 92 " ideal model delta sinusoidal sigma weight residual 93.00 45.62 47.38 1 1.00e+01 1.00e-02 3.10e+01 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 52.92 40.08 1 1.00e+01 1.00e-02 2.25e+01 ... (remaining 16245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 3889 0.122 - 0.245: 231 0.245 - 0.367: 14 0.367 - 0.489: 0 0.489 - 0.611: 3 Chirality restraints: 4137 Sorted by residual: chirality pdb=" C1 NAG Z 1 " pdb=" ND2 ASN O 60 " pdb=" C2 NAG Z 1 " pdb=" O5 NAG Z 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.35e+00 chirality pdb=" C1 NAG V 1 " pdb=" ND2 ASN H 60 " pdb=" C2 NAG V 1 " pdb=" O5 NAG V 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.29e+00 chirality pdb=" C1 NAG d 1 " pdb=" ND2 ASN P 60 " pdb=" C2 NAG d 1 " pdb=" O5 NAG d 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.28e+00 ... (remaining 4134 not shown) Planarity restraints: 4323 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 476 " 0.020 2.00e-02 2.50e+03 3.98e-02 1.58e+01 pdb=" C ARG A 476 " -0.069 2.00e-02 2.50e+03 pdb=" O ARG A 476 " 0.026 2.00e-02 2.50e+03 pdb=" N ASP A 477 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG E 476 " -0.020 2.00e-02 2.50e+03 3.98e-02 1.58e+01 pdb=" C ARG E 476 " 0.069 2.00e-02 2.50e+03 pdb=" O ARG E 476 " -0.025 2.00e-02 2.50e+03 pdb=" N ASP E 477 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG F 476 " -0.020 2.00e-02 2.50e+03 3.97e-02 1.58e+01 pdb=" C ARG F 476 " 0.069 2.00e-02 2.50e+03 pdb=" O ARG F 476 " -0.025 2.00e-02 2.50e+03 pdb=" N ASP F 477 " -0.023 2.00e-02 2.50e+03 ... (remaining 4320 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 210 2.60 - 3.17: 20719 3.17 - 3.75: 37303 3.75 - 4.32: 54597 4.32 - 4.90: 88204 Nonbonded interactions: 201033 Sorted by model distance: nonbonded pdb=" SG CYS F 501 " pdb=" SG CYS I 605 " model vdw 2.025 3.760 nonbonded pdb=" SG CYS E 501 " pdb=" SG CYS G 605 " model vdw 2.025 3.760 nonbonded pdb=" SG CYS I 598 " pdb=" SG CYS I 604 " model vdw 2.026 3.760 nonbonded pdb=" SG CYS G 598 " pdb=" SG CYS G 604 " model vdw 2.026 3.760 nonbonded pdb=" SG CYS Q 23 " pdb=" SG CYS Q 88 " model vdw 2.027 3.760 ... (remaining 201028 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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 'W' selection = chain 'a' } ncs_group { reference = chain 'T' selection = chain 'X' selection = chain 'b' } ncs_group { reference = chain 'U' selection = chain 'Y' selection = chain 'c' } ncs_group { reference = chain 'V' selection = chain 'Z' selection = chain 'd' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.100 Check model and map are aligned: 0.200 Set scattering table: 0.260 Process input model: 56.070 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.160 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 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 0.073 25452 Z= 0.458 Angle : 1.164 11.163 34554 Z= 0.649 Chirality : 0.066 0.611 4137 Planarity : 0.007 0.074 4260 Dihedral : 14.060 107.487 10641 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.57 % Allowed : 5.25 % Favored : 94.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.15), residues: 2979 helix: 0.71 (0.24), residues: 420 sheet: 1.18 (0.17), residues: 861 loop : 0.53 (0.14), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.004 TRP P 47 HIS 0.006 0.002 HIS E 374 PHE 0.023 0.003 PHE E 383 TYR 0.018 0.003 TYR D 36 ARG 0.020 0.002 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 2628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 461 time to evaluate : 2.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 426 MET cc_start: 0.8906 (mtp) cc_final: 0.8621 (mtp) REVERT: L 21 MET cc_start: 0.5719 (mtm) cc_final: 0.5418 (mtm) REVERT: L 24 GLN cc_start: 0.7620 (tt0) cc_final: 0.7208 (tm-30) REVERT: L 58 ILE cc_start: 0.7348 (mm) cc_final: 0.6973 (pt) REVERT: L 75 ILE cc_start: 0.5727 (mt) cc_final: 0.5479 (tt) REVERT: L 85 ASP cc_start: 0.7101 (m-30) cc_final: 0.6445 (m-30) REVERT: L 86 TYR cc_start: 0.8223 (m-80) cc_final: 0.7929 (m-80) REVERT: C 86 ASP cc_start: 0.7786 (m-30) cc_final: 0.7484 (m-30) REVERT: C 94 THR cc_start: 0.8824 (m) cc_final: 0.8466 (p) REVERT: D 69 ASN cc_start: 0.8116 (m-40) cc_final: 0.7690 (m-40) REVERT: E 104 MET cc_start: 0.9467 (ttt) cc_final: 0.9246 (ttt) REVERT: E 426 MET cc_start: 0.8808 (mtp) cc_final: 0.8510 (mmm) REVERT: E 475 MET cc_start: 0.8550 (tpp) cc_final: 0.8342 (mmp) REVERT: O 101 ASP cc_start: 0.7412 (t70) cc_final: 0.7180 (t70) REVERT: Q 21 MET cc_start: 0.5762 (mtm) cc_final: 0.5493 (mtm) REVERT: Q 24 GLN cc_start: 0.7726 (tt0) cc_final: 0.7397 (tm-30) REVERT: Q 75 ILE cc_start: 0.5618 (mt) cc_final: 0.5170 (tt) REVERT: Q 85 ASP cc_start: 0.7311 (m-30) cc_final: 0.6397 (m-30) REVERT: Q 103 ARG cc_start: 0.7744 (mmm160) cc_final: 0.7488 (tpt170) REVERT: J 75 LYS cc_start: 0.9148 (mtpp) cc_final: 0.8942 (mtpt) REVERT: M 6 GLN cc_start: 0.7692 (mt0) cc_final: 0.7341 (mt0) REVERT: M 85 ASP cc_start: 0.8274 (m-30) cc_final: 0.7603 (m-30) REVERT: G 535 MET cc_start: 0.8778 (mtt) cc_final: 0.8404 (mtm) REVERT: G 632 ASP cc_start: 0.8589 (t0) cc_final: 0.8292 (t0) REVERT: F 150 MET cc_start: 0.9018 (mmm) cc_final: 0.8719 (mmt) REVERT: F 426 MET cc_start: 0.8916 (mtp) cc_final: 0.8680 (mtp) REVERT: F 475 MET cc_start: 0.8702 (tpp) cc_final: 0.8241 (mmt) REVERT: R 21 MET cc_start: 0.6214 (mtm) cc_final: 0.5993 (mtt) REVERT: R 24 GLN cc_start: 0.7621 (tt0) cc_final: 0.7332 (tm-30) REVERT: N 74 THR cc_start: 0.7821 (m) cc_final: 0.7429 (p) REVERT: N 85 ASP cc_start: 0.8264 (m-30) cc_final: 0.7835 (m-30) REVERT: I 535 MET cc_start: 0.8654 (mtt) cc_final: 0.8408 (mtp) REVERT: I 657 GLU cc_start: 0.8242 (tt0) cc_final: 0.8007 (tt0) outliers start: 15 outliers final: 3 residues processed: 470 average time/residue: 0.4265 time to fit residues: 295.1469 Evaluate side-chains 336 residues out of total 2628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 333 time to evaluate : 2.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain R residue 4 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 250 optimal weight: 10.0000 chunk 225 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 151 optimal weight: 10.0000 chunk 120 optimal weight: 2.9990 chunk 232 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 173 optimal weight: 4.9990 chunk 269 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 HIS L 17 HIS L 51 ASN L 52 ASN L 89 ASN C 52 ASN D 95 GLN ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 HIS Q 17 HIS Q 52 ASN J 13 GLN J 52 ASN ** G 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 ASN ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 374 HIS R 17 HIS N 6 GLN ** I 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 25452 Z= 0.452 Angle : 0.719 7.128 34554 Z= 0.377 Chirality : 0.051 0.312 4137 Planarity : 0.005 0.047 4260 Dihedral : 10.397 87.419 5238 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.09 % Allowed : 6.74 % Favored : 91.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.66 (0.15), residues: 2979 helix: 1.50 (0.26), residues: 423 sheet: 0.86 (0.17), residues: 876 loop : -0.01 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP O 47 HIS 0.008 0.002 HIS F 105 PHE 0.021 0.002 PHE G 522 TYR 0.018 0.002 TYR J 100G ARG 0.006 0.001 ARG Q 61 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 352 time to evaluate : 2.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8852 (tpp) cc_final: 0.8555 (tpp) REVERT: A 241 ASN cc_start: 0.7622 (OUTLIER) cc_final: 0.7355 (m-40) REVERT: A 475 MET cc_start: 0.8521 (tpp) cc_final: 0.7921 (mmt) REVERT: L 24 GLN cc_start: 0.7689 (tt0) cc_final: 0.7479 (tt0) REVERT: D 79 GLN cc_start: 0.7792 (OUTLIER) cc_final: 0.7064 (mp10) REVERT: B 621 GLU cc_start: 0.8274 (mt-10) cc_final: 0.8005 (mt-10) REVERT: O 3 GLN cc_start: 0.5838 (mp10) cc_final: 0.5596 (mp10) REVERT: Q 4 LEU cc_start: 0.6893 (OUTLIER) cc_final: 0.6586 (tp) REVERT: Q 24 GLN cc_start: 0.7319 (tt0) cc_final: 0.7026 (tm-30) REVERT: Q 86 TYR cc_start: 0.8159 (m-80) cc_final: 0.7564 (m-80) REVERT: M 78 LEU cc_start: 0.7621 (mt) cc_final: 0.7400 (mt) REVERT: M 79 GLN cc_start: 0.7837 (OUTLIER) cc_final: 0.7260 (mp10) REVERT: G 632 ASP cc_start: 0.8973 (t0) cc_final: 0.8689 (t0) REVERT: F 241 ASN cc_start: 0.7200 (OUTLIER) cc_final: 0.6929 (m-40) REVERT: F 475 MET cc_start: 0.8617 (tpp) cc_final: 0.8361 (mmt) REVERT: P 46 GLU cc_start: 0.7209 (mp0) cc_final: 0.6988 (mp0) REVERT: P 100 ASP cc_start: 0.7663 (t0) cc_final: 0.7394 (t0) REVERT: R 4 LEU cc_start: 0.6347 (OUTLIER) cc_final: 0.6119 (tp) REVERT: R 24 GLN cc_start: 0.7503 (tt0) cc_final: 0.7194 (tm-30) REVERT: R 61 ARG cc_start: 0.8613 (mtm-85) cc_final: 0.8389 (ttm110) REVERT: K 13 GLN cc_start: 0.7717 (mm-40) cc_final: 0.7515 (mm110) REVERT: N 79 GLN cc_start: 0.7931 (OUTLIER) cc_final: 0.6988 (mp10) REVERT: N 85 ASP cc_start: 0.8442 (m-30) cc_final: 0.8168 (m-30) outliers start: 55 outliers final: 29 residues processed: 384 average time/residue: 0.4093 time to fit residues: 237.9376 Evaluate side-chains 337 residues out of total 2628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 301 time to evaluate : 2.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 20 SER Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 27 ASP Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 79 GLN Chi-restraints excluded: chain F residue 241 ASN Chi-restraints excluded: chain R residue 4 LEU Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 75 ILE Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 79 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 149 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 224 optimal weight: 0.5980 chunk 183 optimal weight: 8.9990 chunk 74 optimal weight: 1.9990 chunk 270 optimal weight: 2.9990 chunk 291 optimal weight: 1.9990 chunk 240 optimal weight: 0.9990 chunk 267 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 216 optimal weight: 0.1980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 195 ASN D 95 GLN M 17 GLN F 33 ASN ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 17 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25452 Z= 0.197 Angle : 0.572 6.011 34554 Z= 0.300 Chirality : 0.046 0.286 4137 Planarity : 0.004 0.049 4260 Dihedral : 8.963 84.622 5236 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.75 % Allowed : 7.88 % Favored : 90.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.15), residues: 2979 helix: 1.70 (0.27), residues: 423 sheet: 0.94 (0.17), residues: 852 loop : -0.07 (0.14), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP O 47 HIS 0.008 0.001 HIS Q 95B PHE 0.010 0.001 PHE C 29 TYR 0.016 0.001 TYR O 91 ARG 0.006 0.001 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 329 time to evaluate : 3.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.8338 (tpp) cc_final: 0.7801 (mmt) REVERT: H 59 TYR cc_start: 0.6777 (m-10) cc_final: 0.6524 (m-10) REVERT: L 24 GLN cc_start: 0.7691 (tt0) cc_final: 0.7450 (tt0) REVERT: C 86 ASP cc_start: 0.7326 (m-30) cc_final: 0.7083 (m-30) REVERT: D 79 GLN cc_start: 0.7733 (OUTLIER) cc_final: 0.6934 (mp10) REVERT: E 150 MET cc_start: 0.9021 (mmt) cc_final: 0.8754 (mmt) REVERT: E 328 MET cc_start: 0.8951 (ttm) cc_final: 0.8741 (ttt) REVERT: O 91 TYR cc_start: 0.5328 (m-80) cc_final: 0.5089 (m-80) REVERT: M 79 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.7186 (mp10) REVERT: G 632 ASP cc_start: 0.8902 (t0) cc_final: 0.8642 (t0) REVERT: P 100 ASP cc_start: 0.7544 (t0) cc_final: 0.7243 (t0) REVERT: R 61 ARG cc_start: 0.8630 (mtm-85) cc_final: 0.8397 (ttm110) REVERT: N 85 ASP cc_start: 0.8377 (m-30) cc_final: 0.8102 (m-30) REVERT: I 624 ASP cc_start: 0.8959 (m-30) cc_final: 0.8519 (m-30) REVERT: I 657 GLU cc_start: 0.8231 (tt0) cc_final: 0.8018 (tt0) outliers start: 46 outliers final: 31 residues processed: 357 average time/residue: 0.4051 time to fit residues: 219.1723 Evaluate side-chains 334 residues out of total 2628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 301 time to evaluate : 2.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 88 CYS Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain M residue 27 ASP Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 79 GLN Chi-restraints excluded: chain F residue 241 ASN Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 75 ILE Chi-restraints excluded: chain R residue 88 CYS Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 97 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 266 optimal weight: 5.9990 chunk 203 optimal weight: 0.0070 chunk 140 optimal weight: 0.0030 chunk 29 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 181 optimal weight: 4.9990 chunk 271 optimal weight: 7.9990 chunk 287 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 256 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 overall best weight: 2.2014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 GLN L 89 ASN D 95 GLN B 607 ASN B 653 GLN ** G 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 ASN ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 52 ASN ** I 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 25452 Z= 0.444 Angle : 0.653 6.210 34554 Z= 0.339 Chirality : 0.048 0.294 4137 Planarity : 0.005 0.038 4260 Dihedral : 8.545 85.107 5232 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.85 % Allowed : 7.88 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.15), residues: 2979 helix: 1.38 (0.26), residues: 423 sheet: 0.54 (0.17), residues: 876 loop : -0.29 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 479 HIS 0.007 0.002 HIS F 105 PHE 0.020 0.002 PHE K 29 TYR 0.021 0.002 TYR J 27 ARG 0.006 0.001 ARG K 83 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 316 time to evaluate : 3.071 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.8481 (tpp) cc_final: 0.8230 (mmp) REVERT: H 24 VAL cc_start: 0.7403 (OUTLIER) cc_final: 0.7023 (t) REVERT: H 51 ILE cc_start: 0.8472 (OUTLIER) cc_final: 0.8218 (tt) REVERT: H 77 GLN cc_start: 0.8481 (tt0) cc_final: 0.7889 (mm-40) REVERT: L 24 GLN cc_start: 0.7660 (tt0) cc_final: 0.7443 (tt0) REVERT: L 97 LEU cc_start: 0.6953 (tt) cc_final: 0.6732 (tt) REVERT: C 86 ASP cc_start: 0.7265 (m-30) cc_final: 0.6895 (m-30) REVERT: E 150 MET cc_start: 0.9164 (mmt) cc_final: 0.8947 (mmt) REVERT: O 66 ARG cc_start: 0.5326 (ptt90) cc_final: 0.5032 (ptt90) REVERT: G 632 ASP cc_start: 0.8941 (t0) cc_final: 0.8648 (t0) REVERT: F 241 ASN cc_start: 0.7361 (OUTLIER) cc_final: 0.7061 (m-40) REVERT: R 24 GLN cc_start: 0.7480 (tt0) cc_final: 0.7145 (tt0) REVERT: R 54 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7952 (mtp-110) REVERT: R 61 ARG cc_start: 0.8646 (mtm-85) cc_final: 0.8368 (ttm110) REVERT: R 98 PHE cc_start: 0.6412 (OUTLIER) cc_final: 0.4106 (t80) REVERT: K 13 GLN cc_start: 0.7536 (mm-40) cc_final: 0.7285 (mm110) REVERT: N 79 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.7068 (mp10) REVERT: I 624 ASP cc_start: 0.9009 (m-30) cc_final: 0.8574 (m-30) REVERT: I 657 GLU cc_start: 0.8324 (tt0) cc_final: 0.8094 (tt0) outliers start: 75 outliers final: 49 residues processed: 348 average time/residue: 0.4017 time to fit residues: 214.1971 Evaluate side-chains 355 residues out of total 2628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 300 time to evaluate : 2.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 92 ASP Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 58 ILE Chi-restraints excluded: chain Q residue 88 CYS Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 108 LEU 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 ASP Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain F residue 100 MET Chi-restraints excluded: chain F residue 241 ASN Chi-restraints excluded: chain F residue 247 CYS Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 54 ARG Chi-restraints excluded: chain R residue 75 ILE Chi-restraints excluded: chain R residue 98 PHE Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 79 GLN Chi-restraints excluded: chain N residue 97 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 62.8322 > 50: distance: 88 - 274: 3.317 distance: 91 - 271: 5.629 distance: 101 - 258: 11.437 distance: 104 - 255: 11.546 distance: 174 - 199: 9.234 distance: 185 - 214: 7.918 distance: 189 - 190: 4.043 distance: 190 - 191: 7.480 distance: 190 - 199: 5.300 distance: 191 - 222: 33.124 distance: 193 - 194: 6.942 distance: 194 - 195: 7.651 distance: 195 - 196: 4.484 distance: 196 - 197: 5.086 distance: 196 - 198: 4.828 distance: 199 - 200: 5.689 distance: 200 - 201: 5.918 distance: 200 - 203: 6.107 distance: 201 - 202: 8.068 distance: 203 - 204: 5.191 distance: 206 - 207: 5.376 distance: 206 - 209: 3.672 distance: 207 - 208: 8.735 distance: 209 - 210: 4.860 distance: 210 - 211: 6.663 distance: 211 - 212: 4.714 distance: 211 - 213: 9.882 distance: 214 - 215: 11.370 distance: 215 - 216: 15.263 distance: 215 - 218: 6.282 distance: 216 - 217: 23.846 distance: 216 - 222: 40.162 distance: 218 - 219: 8.408 distance: 219 - 220: 21.898 distance: 219 - 221: 20.878 distance: 222 - 223: 16.476 distance: 223 - 224: 35.092 distance: 223 - 226: 11.366 distance: 224 - 225: 19.758 distance: 224 - 234: 11.622 distance: 226 - 227: 12.051 distance: 227 - 228: 5.246 distance: 227 - 229: 8.745 distance: 228 - 230: 5.166 distance: 229 - 231: 6.463 distance: 230 - 232: 4.250 distance: 231 - 232: 8.154 distance: 232 - 233: 4.528 distance: 234 - 235: 4.664 distance: 235 - 236: 8.376 distance: 235 - 238: 4.005 distance: 236 - 237: 12.186 distance: 236 - 243: 5.734 distance: 238 - 239: 15.523 distance: 239 - 240: 10.772 distance: 240 - 241: 12.697 distance: 241 - 242: 5.338 distance: 243 - 244: 5.645 distance: 244 - 245: 6.980 distance: 244 - 247: 8.416 distance: 245 - 246: 7.508 distance: 245 - 255: 3.177 distance: 247 - 248: 3.660 distance: 248 - 249: 13.092 distance: 248 - 250: 14.142 distance: 250 - 252: 3.671 distance: 251 - 253: 18.542 distance: 252 - 253: 9.099 distance: 253 - 254: 4.074 distance: 255 - 256: 3.714 distance: 257 - 258: 4.417 distance: 259 - 260: 4.400 distance: 260 - 261: 3.705 distance: 261 - 262: 7.968 distance: 262 - 263: 13.345 distance: 264 - 265: 3.837 distance: 266 - 267: 5.224 distance: 268 - 269: 4.936 distance: 268 - 270: 5.441 distance: 271 - 272: 5.299 distance: 272 - 273: 7.207 distance: 272 - 275: 5.880 distance: 273 - 274: 10.629 distance: 273 - 278: 7.434 distance: 275 - 276: 10.742 distance: 275 - 277: 9.152