Starting phenix.real_space_refine on Sat Mar 16 18:42:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fyi_29579/03_2024/8fyi_29579.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fyi_29579/03_2024/8fyi_29579.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fyi_29579/03_2024/8fyi_29579.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fyi_29579/03_2024/8fyi_29579.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fyi_29579/03_2024/8fyi_29579.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fyi_29579/03_2024/8fyi_29579.pdb" } resolution = 3.4 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= 0.001 sd= 0.021 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 106 5.16 5 C 9625 2.51 5 N 2621 2.21 5 O 3012 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 87": "OE1" <-> "OE2" Residue "A ASP 149": "OD1" <-> "OD2" Residue "A TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 267": "OE1" <-> "OE2" Residue "A GLU 268": "OE1" <-> "OE2" Residue "A ASP 321": "OD1" <-> "OD2" Residue "A GLU 370": "OE1" <-> "OE2" Residue "B PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 107": "OD1" <-> "OD2" Residue "B TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 269": "OE1" <-> "OE2" Residue "B TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 47": "OD1" <-> "OD2" Residue "C PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 211": "OE1" <-> "OE2" Residue "C TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 584": "OE1" <-> "OE2" Residue "D GLU 654": "OE1" <-> "OE2" Residue "D ASP 659": "OD1" <-> "OD2" Residue "E ASP 632": "OD1" <-> "OD2" Residue "E GLU 634": "OE1" <-> "OE2" Residue "E GLU 654": "OE1" <-> "OE2" Residue "F GLU 634": "OE1" <-> "OE2" Residue "F TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 647": "OE1" <-> "OE2" Residue "F GLU 657": "OE1" <-> "OE2" Residue "Z ASP 56": "OD1" <-> "OD2" Residue "Z GLU 85": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15364 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3407 Classifications: {'peptide': 431} Link IDs: {'PTRANS': 20, 'TRANS': 410} Chain breaks: 6 Chain: "B" Number of atoms: 3433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3433 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 20, 'TRANS': 413} Chain breaks: 5 Chain: "C" Number of atoms: 3433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3433 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 20, 'TRANS': 413} Chain breaks: 5 Chain: "D" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 982 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "E" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 982 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "F" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 982 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "Z" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1370 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 6, 'TRANS': 169} Chain: "G" 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: "H" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: "I" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} 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: "J" 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: "K" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: "L" 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: "M" 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: "N" 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: "O" 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: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" 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: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 8.11, per 1000 atoms: 0.53 Number of scatterers: 15364 At special positions: 0 Unit cell: (125.632, 123.968, 143.936, 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 106 16.00 O 3012 8.00 N 2621 7.00 C 9625 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.04 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.04 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 D 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 74 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.03 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS E 605 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.05 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 16 " - pdb=" SG CYS Z 84 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 130 " - pdb=" SG CYS Z 159 " 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=1, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " BMA H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 3 " - " NAG I 4 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " BMA K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 133 " " NAG A 603 " - " ASN A 160 " " NAG A 604 " - " ASN A 197 " " NAG A 605 " - " ASN A 234 " " NAG A 606 " - " ASN A 262 " " NAG A 608 " - " ASN A 276 " " NAG A 609 " - " ASN A 295 " " NAG A 610 " - " ASN A 301 " " NAG A 611 " - " ASN A 392 " " NAG A 612 " - " ASN A 448 " " NAG B 601 " - " ASN B 88 " " NAG B 602 " - " ASN B 133 " " NAG B 603 " - " ASN B 160 " " NAG B 604 " - " ASN B 197 " " NAG B 605 " - " ASN B 234 " " NAG B 606 " - " ASN B 262 " " NAG B 608 " - " ASN B 276 " " NAG B 609 " - " ASN B 295 " " NAG B 610 " - " ASN B 301 " " NAG B 611 " - " ASN B 363 " " NAG B 612 " - " ASN B 392 " " NAG B 613 " - " ASN B 448 " " NAG C 601 " - " ASN C 133 " " NAG C 602 " - " ASN C 160 " " NAG C 603 " - " ASN C 197 " " NAG C 604 " - " ASN C 234 " " NAG C 607 " - " ASN C 301 " " NAG C 608 " - " ASN C 363 " " NAG C 609 " - " ASN C 392 " " NAG C 610 " - " ASN C 448 " " NAG G 1 " - " ASN A 156 " " NAG I 1 " - " ASN A 386 " " NAG I 3 " - " ASN A 363 " " NAG J 1 " - " ASN B 156 " " NAG L 1 " - " ASN B 386 " " NAG M 1 " - " ASN C 156 " " NAG N 1 " - " ASN C 262 " " NAG O 1 " - " ASN C 386 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.15 Conformation dependent library (CDL) restraints added in 2.7 seconds 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3448 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 32 sheets defined 24.7% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.68 Creating SS restraints... Processing helix chain 'A' and resid 98 through 115 removed outlier: 4.242A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 335 through 354 removed outlier: 4.182A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE A 353 " --> pdb=" O LEU A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 390 Processing helix chain 'A' and resid 475 through 481 removed outlier: 3.682A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 74 Processing helix chain 'B' and resid 98 through 115 removed outlier: 4.117A pdb=" N GLU B 102 " --> pdb=" O ASN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 126 Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 335 through 350 Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 368 through 373 Processing helix chain 'B' and resid 474 through 481 removed outlier: 3.811A pdb=" N ASN B 478 " --> pdb=" O ASP B 474 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER B 481 " --> pdb=" O ASP B 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 74 Processing helix chain 'C' and resid 98 through 115 removed outlier: 4.175A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 354 removed outlier: 3.763A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 377 through 381 Processing helix chain 'C' and resid 386 through 390 removed outlier: 4.499A pdb=" N GLY C 389 " --> pdb=" O ASN C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 480 removed outlier: 3.526A pdb=" N ASN C 478 " --> pdb=" O ASP C 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 542 removed outlier: 3.920A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 595 removed outlier: 3.546A pdb=" N LYS D 574 " --> pdb=" O VAL D 570 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP D 589 " --> pdb=" O ARG D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 624 Processing helix chain 'D' and resid 627 through 636 Processing helix chain 'D' and resid 638 through 662 Processing helix chain 'E' and resid 529 through 534 Processing helix chain 'E' and resid 536 through 543 removed outlier: 3.814A pdb=" N GLN E 540 " --> pdb=" O THR E 536 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASN E 543 " --> pdb=" O VAL E 539 " (cutoff:3.500A) Processing helix chain 'E' and resid 570 through 596 removed outlier: 3.602A pdb=" N ASP E 589 " --> pdb=" O ARG E 585 " (cutoff:3.500A) Processing helix chain 'E' and resid 618 through 623 Processing helix chain 'E' and resid 627 through 636 Processing helix chain 'E' and resid 638 through 662 removed outlier: 3.552A pdb=" N ILE E 642 " --> pdb=" O TYR E 638 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 528 removed outlier: 4.282A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 536 Processing helix chain 'F' and resid 536 through 543 removed outlier: 4.157A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 595 removed outlier: 3.707A pdb=" N LYS F 574 " --> pdb=" O VAL F 570 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 623 removed outlier: 3.501A pdb=" N ILE F 622 " --> pdb=" O ASN F 618 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TRP F 623 " --> pdb=" O LEU F 619 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 618 through 623' Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 662 removed outlier: 3.766A pdb=" N ALA F 662 " --> pdb=" O GLN F 658 " (cutoff:3.500A) Processing helix chain 'Z' and resid 58 through 62 removed outlier: 3.628A pdb=" N TRP Z 62 " --> pdb=" O ARG Z 59 " (cutoff:3.500A) Processing helix chain 'Z' and resid 75 through 79 removed outlier: 3.680A pdb=" N SER Z 79 " --> pdb=" O ILE Z 76 " (cutoff:3.500A) Processing helix chain 'Z' and resid 150 through 154 removed outlier: 3.764A pdb=" N SER Z 154 " --> pdb=" O LEU Z 151 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.274A pdb=" N VAL A 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.791A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AA4, first strand: chain 'A' and resid 66 through 67 removed outlier: 7.346A pdb=" N HIS A 66 " --> pdb=" O SER A 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.509A pdb=" N GLY A 237 " --> pdb=" O PHE A 93 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 169 through 177 removed outlier: 3.827A pdb=" N LYS A 189 " --> pdb=" O CYS A 131 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 201 through 203 Processing sheet with id=AA8, 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 302 removed outlier: 7.226A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 329 through 334 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 470 Processing sheet with id=AA9, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.603A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 494 through 499 removed outlier: 5.007A pdb=" N VAL B 36 " --> pdb=" O THR E 606 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR E 606 " --> pdb=" O VAL B 36 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 45 through 47 removed outlier: 4.338A pdb=" N VAL B 242 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 53 through 55 Processing sheet with id=AB4, first strand: chain 'B' and resid 91 through 94 removed outlier: 3.574A pdb=" N GLU B 91 " --> pdb=" O CYS B 239 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 169 through 177 removed outlier: 3.508A pdb=" N CYS B 131 " --> pdb=" O LYS B 189 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LYS B 189 " --> pdb=" O CYS B 131 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 200 through 203 removed outlier: 6.217A pdb=" N ALA B 200 " --> pdb=" O ALA B 433 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N TYR B 435 " --> pdb=" O ALA B 200 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N THR B 202 " --> pdb=" O TYR B 435 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 271 through 274 removed outlier: 6.203A pdb=" N ILE B 358 " --> pdb=" O GLU B 466 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N PHE B 468 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ARG B 360 " --> pdb=" O PHE B 468 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 374 through 378 removed outlier: 3.812A pdb=" N CYS B 378 " --> pdb=" O GLU B 381 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU B 381 " --> pdb=" O CYS B 378 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N PHE B 382 " --> pdb=" O LYS B 421 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N SER B 334 " --> pdb=" O GLN B 293 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N GLN B 293 " --> pdb=" O SER B 334 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE B 443 " --> pdb=" O ARG B 298 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ASN B 300 " --> pdb=" O GLY B 441 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N GLY B 441 " --> pdb=" O ASN B 300 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 304 through 312 removed outlier: 3.568A pdb=" N ILE B 309 " --> pdb=" O GLN B 315 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N GLN B 315 " --> pdb=" O ILE B 309 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 494 through 499 removed outlier: 4.780A pdb=" N VAL F 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N VAL C 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N THR F 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N TYR C 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N CYS F 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AC3, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AC4, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.694A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 169 through 177 removed outlier: 3.814A pdb=" N LYS C 189 " --> pdb=" O CYS C 131 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.046A pdb=" N ALA C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N TYR C 435 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 260 through 261 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 260 through 261 current: chain 'C' and resid 284 through 302 removed outlier: 3.912A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 322 through 323 current: chain 'C' and resid 393 through 395 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 393 through 395 current: chain 'C' and resid 465 through 470 Processing sheet with id=AC8, first strand: chain 'C' and resid 305 through 312 removed outlier: 7.202A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 382 through 383 removed outlier: 4.259A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'Z' and resid 2 through 5 removed outlier: 3.803A pdb=" N LYS Z 2 " --> pdb=" O GLU Z 92 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'Z' and resid 13 through 15 removed outlier: 3.561A pdb=" N LEU Z 14 " --> pdb=" O LEU Z 69 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'Z' and resid 27 through 29 removed outlier: 6.659A pdb=" N TRP Z 28 " --> pdb=" O ILE Z 36 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'Z' and resid 99 through 102 Processing sheet with id=AD5, first strand: chain 'Z' and resid 139 through 140 removed outlier: 3.762A pdb=" N GLY Z 140 " --> pdb=" O VAL Z 128 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL Z 128 " --> pdb=" O GLY Z 140 " (cutoff:3.500A) 483 hydrogen bonds defined for protein. 1317 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: 4.75 Time building geometry restraints manager: 6.70 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: 4896 1.35 - 1.48: 3914 1.48 - 1.61: 6694 1.61 - 1.75: 0 1.75 - 1.88: 142 Bond restraints: 15646 Sorted by residual: bond pdb=" C1 NAG C 605 " pdb=" O5 NAG C 605 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.48e+00 bond pdb=" CB CYS C 331 " pdb=" SG CYS C 331 " ideal model delta sigma weight residual 1.808 1.879 -0.071 3.30e-02 9.18e+02 4.58e+00 bond pdb=" C LYS C 117 " pdb=" N PRO C 118 " ideal model delta sigma weight residual 1.334 1.348 -0.015 8.40e-03 1.42e+04 3.13e+00 bond pdb=" CB CYS C 296 " pdb=" SG CYS C 296 " ideal model delta sigma weight residual 1.808 1.752 0.056 3.30e-02 9.18e+02 2.92e+00 bond pdb=" C1 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.83e+00 ... (remaining 15641 not shown) Histogram of bond angle deviations from ideal: 99.04 - 106.04: 287 106.04 - 113.04: 9027 113.04 - 120.04: 4975 120.04 - 127.04: 6696 127.04 - 134.04: 216 Bond angle restraints: 21201 Sorted by residual: angle pdb=" C SER F 612 " pdb=" CA SER F 612 " pdb=" CB SER F 612 " ideal model delta sigma weight residual 116.54 110.53 6.01 1.15e+00 7.56e-01 2.73e+01 angle pdb=" CB MET B 475 " pdb=" CG MET B 475 " pdb=" SD MET B 475 " ideal model delta sigma weight residual 112.70 127.27 -14.57 3.00e+00 1.11e-01 2.36e+01 angle pdb=" CA CYS C 296 " pdb=" CB CYS C 296 " pdb=" SG CYS C 296 " ideal model delta sigma weight residual 114.40 125.19 -10.79 2.30e+00 1.89e-01 2.20e+01 angle pdb=" CA CYS C 501 " pdb=" CB CYS C 501 " pdb=" SG CYS C 501 " ideal model delta sigma weight residual 114.40 123.26 -8.86 2.30e+00 1.89e-01 1.48e+01 angle pdb=" CB GLN B 348 " pdb=" CG GLN B 348 " pdb=" CD GLN B 348 " ideal model delta sigma weight residual 112.60 119.14 -6.54 1.70e+00 3.46e-01 1.48e+01 ... (remaining 21196 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.58: 9201 22.58 - 45.15: 803 45.15 - 67.73: 119 67.73 - 90.31: 39 90.31 - 112.88: 15 Dihedral angle restraints: 10177 sinusoidal: 4868 harmonic: 5309 Sorted by residual: dihedral pdb=" CB CYS B 501 " pdb=" SG CYS B 501 " pdb=" SG CYS E 605 " pdb=" CB CYS E 605 " ideal model delta sinusoidal sigma weight residual 93.00 8.34 84.66 1 1.00e+01 1.00e-02 8.71e+01 dihedral pdb=" CB CYS C 501 " pdb=" SG CYS C 501 " pdb=" SG CYS F 605 " pdb=" CB CYS F 605 " ideal model delta sinusoidal sigma weight residual -86.00 -14.23 -71.77 1 1.00e+01 1.00e-02 6.60e+01 dihedral pdb=" CB CYS B 126 " pdb=" SG CYS B 126 " pdb=" SG CYS B 196 " pdb=" CB CYS B 196 " ideal model delta sinusoidal sigma weight residual 93.00 160.06 -67.06 1 1.00e+01 1.00e-02 5.86e+01 ... (remaining 10174 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.149: 2532 0.149 - 0.297: 19 0.297 - 0.446: 0 0.446 - 0.594: 1 0.594 - 0.743: 1 Chirality restraints: 2553 Sorted by residual: chirality pdb=" C1 NAG C 610 " pdb=" ND2 ASN C 448 " pdb=" C2 NAG C 610 " pdb=" O5 NAG C 610 " both_signs ideal model delta sigma weight residual False -2.40 -1.66 -0.74 2.00e-01 2.50e+01 1.38e+01 chirality pdb=" C1 NAG B 612 " pdb=" ND2 ASN B 392 " pdb=" C2 NAG B 612 " pdb=" O5 NAG B 612 " both_signs ideal model delta sigma weight residual False -2.40 -1.83 -0.57 2.00e-01 2.50e+01 8.00e+00 chirality pdb=" C5 BMA H 2 " pdb=" C4 BMA H 2 " pdb=" C6 BMA H 2 " pdb=" O5 BMA H 2 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 2550 not shown) Planarity restraints: 2658 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 75 " 0.057 5.00e-02 4.00e+02 8.62e-02 1.19e+01 pdb=" N PRO B 76 " -0.149 5.00e-02 4.00e+02 pdb=" CA PRO B 76 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 76 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 75 " 0.036 5.00e-02 4.00e+02 5.54e-02 4.91e+00 pdb=" N PRO A 76 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 76 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 76 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 448 " 0.020 2.00e-02 2.50e+03 1.97e-02 4.83e+00 pdb=" CG ASN C 448 " -0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN C 448 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN C 448 " -0.019 2.00e-02 2.50e+03 pdb=" C1 NAG C 610 " 0.019 2.00e-02 2.50e+03 ... (remaining 2655 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1348 2.74 - 3.28: 14452 3.28 - 3.82: 24907 3.82 - 4.36: 28874 4.36 - 4.90: 51384 Nonbonded interactions: 120965 Sorted by model distance: nonbonded pdb=" O SER A 264 " pdb=" NE2 GLN A 287 " model vdw 2.200 2.520 nonbonded pdb=" O LEU A 369 " pdb=" OG1 THR A 373 " model vdw 2.229 2.440 nonbonded pdb=" OG1 THR C 297 " pdb=" O ILE C 443 " model vdw 2.249 2.440 nonbonded pdb=" NH1 ARG C 273 " pdb=" OE1 GLN C 287 " model vdw 2.251 2.520 nonbonded pdb=" NZ LYS E 655 " pdb=" OE1 GLN E 658 " model vdw 2.252 2.520 ... (remaining 120960 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 34 through 367 or resid 369 through 504 or resid 601 throu \ gh 610)) selection = (chain 'B' and (resid 34 through 367 or resid 369 through 428 or resid 432 throu \ gh 504 or resid 601 through 610)) selection = (chain 'C' and (resid 34 through 367 or resid 369 through 428 or resid 432 throu \ gh 504 or resid 601 through 610)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = (chain 'G' and resid 1) selection = (chain 'H' and resid 1) selection = (chain 'J' and resid 1) selection = (chain 'K' and resid 1) selection = (chain 'L' and resid 1) selection = (chain 'M' and resid 1) selection = (chain 'O' and resid 1) } 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: 3.330 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: 0.010 Extract box with map and model: 10.620 Check model and map are aligned: 0.230 Set scattering table: 0.160 Process input model: 41.140 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.090 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: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 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 : 0.005 0.071 15646 Z= 0.289 Angle : 0.684 14.570 21201 Z= 0.346 Chirality : 0.051 0.743 2553 Planarity : 0.004 0.086 2619 Dihedral : 16.635 112.883 6624 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.18 % Allowed : 21.97 % Favored : 77.85 % 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: -1.26 (0.20), residues: 1792 helix: 0.36 (0.27), residues: 415 sheet: -1.16 (0.23), residues: 539 loop : -1.12 (0.20), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 96 HIS 0.003 0.000 HIS C 374 PHE 0.022 0.001 PHE C 53 TYR 0.011 0.001 TYR A 435 ARG 0.005 0.000 ARG E 617 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 224 time to evaluate : 1.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 475 MET cc_start: 0.8569 (mmm) cc_final: 0.8345 (mmm) REVERT: Z 136 LYS cc_start: 0.7529 (mptt) cc_final: 0.7250 (pttm) REVERT: Z 165 GLN cc_start: 0.8064 (mt0) cc_final: 0.7689 (tm-30) outliers start: 3 outliers final: 3 residues processed: 226 average time/residue: 0.2677 time to fit residues: 91.8597 Evaluate side-chains 213 residues out of total 1643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 210 time to evaluate : 1.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain E residue 627 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 6.9990 chunk 137 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 142 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 chunk 165 optimal weight: 10.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 575 GLN D 577 GLN F 575 GLN F 590 GLN F 611 ASN ** Z 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.0782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 15646 Z= 0.351 Angle : 0.609 9.150 21201 Z= 0.304 Chirality : 0.048 0.514 2553 Planarity : 0.004 0.063 2619 Dihedral : 8.738 62.910 3119 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.65 % Allowed : 20.82 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.20), residues: 1792 helix: 0.73 (0.27), residues: 399 sheet: -1.12 (0.23), residues: 540 loop : -1.10 (0.20), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 96 HIS 0.003 0.001 HIS C 374 PHE 0.012 0.002 PHE C 159 TYR 0.014 0.002 TYR A 484 ARG 0.004 0.000 ARG B 429 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 217 time to evaluate : 1.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 348 GLN cc_start: 0.7982 (tm-30) cc_final: 0.7700 (tm-30) REVERT: C 164 GLU cc_start: 0.7917 (pm20) cc_final: 0.7672 (pm20) REVERT: Z 136 LYS cc_start: 0.7648 (mptt) cc_final: 0.7415 (pttm) REVERT: Z 165 GLN cc_start: 0.8143 (mt0) cc_final: 0.7830 (tm-30) outliers start: 60 outliers final: 40 residues processed: 256 average time/residue: 0.2502 time to fit residues: 98.0960 Evaluate side-chains 244 residues out of total 1643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 204 time to evaluate : 1.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 622 ILE Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain Z residue 23 SER Chi-restraints excluded: chain Z residue 76 ILE Chi-restraints excluded: chain Z residue 142 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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: 57.9541 > 50: distance: 17 - 24: 5.974 distance: 24 - 25: 5.967 distance: 24 - 173: 4.431 distance: 25 - 26: 3.365 distance: 25 - 28: 6.291 distance: 26 - 27: 11.660 distance: 26 - 35: 3.475 distance: 27 - 170: 7.039 distance: 28 - 29: 7.087 distance: 29 - 30: 4.197 distance: 29 - 31: 8.783 distance: 30 - 32: 8.646 distance: 31 - 33: 3.620 distance: 32 - 34: 5.387 distance: 33 - 34: 6.183 distance: 35 - 36: 3.400 distance: 36 - 37: 11.255 distance: 36 - 39: 14.325 distance: 37 - 38: 11.873 distance: 39 - 40: 16.498 distance: 40 - 41: 12.490 distance: 40 - 42: 15.256 distance: 43 - 44: 5.900 distance: 44 - 45: 12.010 distance: 44 - 47: 5.388 distance: 45 - 51: 13.757 distance: 47 - 48: 4.291 distance: 48 - 49: 7.368 distance: 49 - 50: 16.651 distance: 51 - 52: 7.279 distance: 52 - 53: 10.078 distance: 52 - 55: 10.745 distance: 53 - 54: 13.254 distance: 53 - 65: 11.161 distance: 55 - 56: 6.437 distance: 56 - 57: 6.339 distance: 56 - 58: 8.465 distance: 57 - 59: 9.532 distance: 58 - 60: 13.819 distance: 58 - 61: 6.490 distance: 59 - 60: 10.138 distance: 60 - 62: 5.938 distance: 61 - 63: 9.967 distance: 62 - 64: 9.734 distance: 63 - 64: 10.228 distance: 65 - 66: 13.828 distance: 66 - 67: 4.224 distance: 66 - 69: 20.483 distance: 67 - 68: 32.102 distance: 67 - 74: 22.677 distance: 69 - 70: 18.614 distance: 70 - 71: 10.235 distance: 71 - 72: 15.669 distance: 72 - 73: 26.800 distance: 74 - 75: 7.488 distance: 75 - 76: 11.164 distance: 75 - 78: 8.360 distance: 76 - 77: 37.479 distance: 76 - 82: 11.420 distance: 78 - 79: 21.175 distance: 79 - 80: 12.593 distance: 79 - 81: 32.297 distance: 82 - 83: 23.719 distance: 83 - 84: 14.428 distance: 83 - 86: 17.638 distance: 84 - 85: 8.952 distance: 84 - 90: 5.470 distance: 85 - 114: 16.239 distance: 86 - 87: 27.243 distance: 87 - 88: 16.929 distance: 87 - 89: 15.166 distance: 90 - 91: 11.451 distance: 91 - 92: 25.170 distance: 91 - 94: 20.183 distance: 92 - 93: 32.494 distance: 92 - 98: 11.237 distance: 93 - 123: 27.700 distance: 94 - 95: 20.034 distance: 95 - 96: 10.145 distance: 96 - 97: 43.390 distance: 98 - 99: 27.246 distance: 99 - 100: 29.846 distance: 99 - 102: 32.752 distance: 100 - 101: 36.025 distance: 100 - 105: 6.167 distance: 101 - 129: 32.640 distance: 102 - 103: 25.505 distance: 102 - 104: 33.221 distance: 105 - 106: 6.246 distance: 106 - 107: 16.315 distance: 106 - 109: 13.408 distance: 107 - 108: 13.253 distance: 107 - 114: 6.279 distance: 108 - 134: 12.414 distance: 109 - 110: 23.783 distance: 110 - 111: 19.248 distance: 111 - 112: 20.887 distance: 111 - 113: 13.037