Starting phenix.real_space_refine (version: dev) on Tue Feb 21 23:29:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8y_23240/02_2023/7l8y_23240_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8y_23240/02_2023/7l8y_23240.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8y_23240/02_2023/7l8y_23240.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8y_23240/02_2023/7l8y_23240.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8y_23240/02_2023/7l8y_23240_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8y_23240/02_2023/7l8y_23240_updated.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 585": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 15903 Number of models: 1 Model: "" Number of chains: 27 Chain: "H" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 565 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 113} Link IDs: {'TRANS': 112} Unresolved non-hydrogen bonds: 226 Unresolved non-hydrogen angles: 339 Unresolved non-hydrogen dihedrals: 113 Planarities with less than four sites: {'UNK:plan-1': 113} Unresolved non-hydrogen planarities: 113 Chain: "L" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 495 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'TRANS': 98} Unresolved non-hydrogen bonds: 198 Unresolved non-hydrogen angles: 297 Unresolved non-hydrogen dihedrals: 99 Planarities with less than four sites: {'UNK:plan-1': 99} Unresolved non-hydrogen planarities: 99 Chain: "C" Number of atoms: 3447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3447 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 20, 'TRANS': 416} Chain breaks: 3 Chain: "D" Number of atoms: 1131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1131 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 2, 'TRANS': 139} Chain: "A" Number of atoms: 3460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3460 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 20, 'TRANS': 418} Chain breaks: 3 Chain: "B" Number of atoms: 1139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1139 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain: "E" Number of atoms: 3434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3434 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 20, 'TRANS': 414} Chain breaks: 3 Chain: "F" Number of atoms: 1139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1139 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} 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 chiralities: 2 Chain: "I" 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 chiralities: 2 Chain: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 5 Chain: "K" 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 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 chiralities: 2 Chain: "N" 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 chiralities: 2 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 chiralities: 2 Chain: "P" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 5 Chain: "Q" 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 chiralities: 2 Chain: "R" 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 chiralities: 2 Chain: "S" 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 chiralities: 2 Chain: "T" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 5 Chain: "U" 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 chiralities: 2 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen chiralities: 15 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" 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 chiralities: 14 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 9.68, per 1000 atoms: 0.61 Number of scatterers: 15903 At special positions: 0 Unit cell: (133.9, 161.71, 123.6, 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 105 16.00 O 3186 8.00 N 2711 7.00 C 9901 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 73 " distance=2.03 Simple disulfide: pdb=" SG CYS C 74 " - pdb=" SG CYS D 561 " distance=2.02 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.02 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=2.01 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.01 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 D 605 " distance=2.04 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.03 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS B 561 " distance=2.02 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 73 " distance=2.03 Simple disulfide: pdb=" SG CYS E 74 " - pdb=" SG CYS F 561 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.06 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.02 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.02 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.02 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA J 3 " - " MAN J 4 " " BMA P 3 " - " MAN P 4 " " BMA T 3 " - " MAN T 4 " ALPHA1-6 " BMA J 3 " - " MAN J 5 " " BMA P 3 " - " MAN P 5 " " BMA T 3 " - " MAN T 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 234 " " NAG A 603 " - " ASN A 241 " " NAG A 604 " - " ASN A 276 " " NAG A 605 " - " ASN A 392 " " NAG A 606 " - " ASN A 295 " " NAG A 607 " - " ASN A 448 " " NAG A 608 " - " ASN A 301 " " NAG A 609 " - " ASN A 160 " " NAG A 610 " - " ASN A 197 " " NAG A 611 " - " ASN A 133 " " NAG A 612 " - " ASN A 355 " " NAG A 613 " - " ASN A 289 " " NAG A 614 " - " ASN A 462 " " NAG A 615 " - " ASN A 339 " " NAG B 701 " - " ASN B 637 " " NAG B 702 " - " ASN B 611 " " NAG C 601 " - " ASN C 234 " " NAG C 602 " - " ASN C 241 " " NAG C 603 " - " ASN C 339 " " NAG C 604 " - " ASN C 332 " " NAG C 605 " - " ASN C 295 " " NAG C 606 " - " ASN C 448 " " NAG C 607 " - " ASN C 301 " " NAG C 608 " - " ASN C 197 " " NAG C 609 " - " ASN C 133 " " NAG C 610 " - " ASN C 289 " " NAG C 611 " - " ASN C 137 " " NAG D 701 " - " ASN D 637 " " NAG D 702 " - " ASN D 611 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 234 " " NAG E 603 " - " ASN E 241 " " NAG E 604 " - " ASN E 276 " " NAG E 605 " - " ASN E 392 " " NAG E 606 " - " ASN E 339 " " NAG E 607 " - " ASN E 295 " " NAG E 608 " - " ASN E 448 " " NAG E 609 " - " ASN E 301 " " NAG E 610 " - " ASN E 160 " " NAG E 611 " - " ASN E 197 " " NAG E 612 " - " ASN E 133 " " NAG E 613 " - " ASN E 355 " " NAG E 614 " - " ASN E 289 " " NAG F 701 " - " ASN F 611 " " NAG G 1 " - " ASN C 392 " " NAG I 1 " - " ASN C 386 " " NAG J 1 " - " ASN C 262 " " NAG K 1 " - " ASN C 156 " " NAG M 1 " - " ASN C 160 " " NAG N 1 " - " ASN A 386 " " NAG O 1 " - " ASN A 332 " " NAG P 1 " - " ASN A 262 " " NAG Q 1 " - " ASN A 156 " " NAG R 1 " - " ASN E 386 " " NAG S 1 " - " ASN E 332 " " NAG T 1 " - " ASN E 262 " " NAG U 1 " - " ASN E 156 " Time building additional restraints: 7.27 Conformation dependent library (CDL) restraints added in 2.2 seconds 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3680 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 36 sheets defined 29.7% alpha, 25.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.07 Creating SS restraints... Processing helix chain 'L' and resid 28 through 30 No H-bonds generated for 'chain 'L' and resid 28 through 30' Processing helix chain 'L' and resid 60 through 62 No H-bonds generated for 'chain 'L' and resid 60 through 62' Processing helix chain 'L' and resid 80 through 82 No H-bonds generated for 'chain 'L' and resid 80 through 82' Processing helix chain 'C' and resid 68 through 72 Processing helix chain 'C' and resid 99 through 115 Processing helix chain 'C' and resid 123 through 125 No H-bonds generated for 'chain 'C' and resid 123 through 125' Processing helix chain 'C' and resid 140 through 150 No H-bonds generated for 'chain 'C' and resid 140 through 150' Processing helix chain 'C' and resid 178 through 180 No H-bonds generated for 'chain 'C' and resid 178 through 180' Processing helix chain 'C' and resid 335 through 352 removed outlier: 4.219A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 372 No H-bonds generated for 'chain 'C' and resid 369 through 372' Processing helix chain 'C' and resid 388 through 390 No H-bonds generated for 'chain 'C' and resid 388 through 390' Processing helix chain 'C' and resid 475 through 485 removed outlier: 3.776A pdb=" N ARG C 480 " --> pdb=" O ASP C 477 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N SER C 481 " --> pdb=" O ASN C 478 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N TYR C 484 " --> pdb=" O SER C 481 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LYS C 485 " --> pdb=" O GLU C 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 530 through 565 removed outlier: 4.402A pdb=" N MET D 535 " --> pdb=" O GLY D 531 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N THR D 536 " --> pdb=" O ALA D 532 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LEU D 537 " --> pdb=" O ALA D 533 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N THR D 538 " --> pdb=" O SER D 534 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N VAL D 539 " --> pdb=" O MET D 535 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LEU D 544 " --> pdb=" O GLN D 540 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N LEU D 545 " --> pdb=" O ALA D 541 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE D 548 " --> pdb=" O LEU D 544 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG D 557 " --> pdb=" O SER D 553 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ALA D 558 " --> pdb=" O ASN D 554 " (cutoff:3.500A) Proline residue: D 559 - end of helix removed outlier: 4.036A pdb=" N GLN D 562 " --> pdb=" O ALA D 558 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLN D 563 " --> pdb=" O PRO D 559 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N HIS D 564 " --> pdb=" O GLU D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 595 Processing helix chain 'D' and resid 621 through 624 No H-bonds generated for 'chain 'D' and resid 621 through 624' Processing helix chain 'D' and resid 628 through 634 Processing helix chain 'D' and resid 636 through 661 removed outlier: 4.109A pdb=" N THR D 639 " --> pdb=" O SER D 636 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N GLN D 640 " --> pdb=" O ASN D 637 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N TYR D 643 " --> pdb=" O GLN D 640 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU D 654 " --> pdb=" O ASN D 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 71 No H-bonds generated for 'chain 'A' and resid 68 through 71' Processing helix chain 'A' and resid 95 through 97 No H-bonds generated for 'chain 'A' and resid 95 through 97' Processing helix chain 'A' and resid 99 through 116 removed outlier: 3.563A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 125 No H-bonds generated for 'chain 'A' and resid 123 through 125' Processing helix chain 'A' and resid 140 through 150 No H-bonds generated for 'chain 'A' and resid 140 through 150' Processing helix chain 'A' and resid 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 335 through 353 removed outlier: 3.935A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 390 No H-bonds generated for 'chain 'A' and resid 388 through 390' Processing helix chain 'A' and resid 475 through 485 removed outlier: 4.396A pdb=" N SER A 481 " --> pdb=" O ASN A 478 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N TYR A 484 " --> pdb=" O SER A 481 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LYS A 485 " --> pdb=" O GLU A 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 567 removed outlier: 5.219A pdb=" N THR B 538 " --> pdb=" O MET B 535 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN B 540 " --> pdb=" O LEU B 537 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG B 542 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU B 544 " --> pdb=" O ALA B 541 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER B 546 " --> pdb=" O ASN B 543 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N GLY B 547 " --> pdb=" O LEU B 544 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU B 556 " --> pdb=" O SER B 553 " (cutoff:3.500A) Proline residue: B 559 - end of helix removed outlier: 4.387A pdb=" N GLN B 563 " --> pdb=" O GLU B 560 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU B 566 " --> pdb=" O GLN B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 595 Processing helix chain 'B' and resid 620 through 623 No H-bonds generated for 'chain 'B' and resid 620 through 623' Processing helix chain 'B' and resid 628 through 634 Processing helix chain 'B' and resid 636 through 661 removed outlier: 5.153A pdb=" N GLN B 640 " --> pdb=" O ASN B 637 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU B 654 " --> pdb=" O ASN B 651 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 72 Processing helix chain 'E' and resid 95 through 97 No H-bonds generated for 'chain 'E' and resid 95 through 97' Processing helix chain 'E' and resid 99 through 115 Processing helix chain 'E' and resid 123 through 125 No H-bonds generated for 'chain 'E' and resid 123 through 125' Processing helix chain 'E' and resid 178 through 180 No H-bonds generated for 'chain 'E' and resid 178 through 180' Processing helix chain 'E' and resid 335 through 352 removed outlier: 4.237A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 372 No H-bonds generated for 'chain 'E' and resid 369 through 372' Processing helix chain 'E' and resid 388 through 390 No H-bonds generated for 'chain 'E' and resid 388 through 390' Processing helix chain 'E' and resid 475 through 485 removed outlier: 4.538A pdb=" N SER E 481 " --> pdb=" O ASN E 478 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N TYR E 484 " --> pdb=" O SER E 481 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LYS E 485 " --> pdb=" O GLU E 482 " (cutoff:3.500A) Processing helix chain 'F' and resid 530 through 567 removed outlier: 4.813A pdb=" N MET F 535 " --> pdb=" O GLY F 531 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N THR F 536 " --> pdb=" O ALA F 532 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LEU F 537 " --> pdb=" O ALA F 533 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N THR F 538 " --> pdb=" O SER F 534 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N VAL F 539 " --> pdb=" O MET F 535 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU F 544 " --> pdb=" O GLN F 540 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N LEU F 545 " --> pdb=" O ALA F 541 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ALA F 558 " --> pdb=" O ASN F 554 " (cutoff:3.500A) Proline residue: F 559 - end of helix removed outlier: 5.095A pdb=" N HIS F 564 " --> pdb=" O GLU F 560 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU F 565 " --> pdb=" O CYS F 561 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU F 566 " --> pdb=" O GLN F 562 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N LYS F 567 " --> pdb=" O GLN F 563 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 595 Processing helix chain 'F' and resid 612 through 615 No H-bonds generated for 'chain 'F' and resid 612 through 615' Processing helix chain 'F' and resid 619 through 621 No H-bonds generated for 'chain 'F' and resid 619 through 621' Processing helix chain 'F' and resid 628 through 662 removed outlier: 4.511A pdb=" N LYS F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU F 634 " --> pdb=" O GLN F 630 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ASN F 637 " --> pdb=" O LYS F 633 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N TYR F 638 " --> pdb=" O GLU F 634 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N THR F 639 " --> pdb=" O ILE F 635 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N GLN F 640 " --> pdb=" O SER F 636 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ILE F 641 " --> pdb=" O ASN F 637 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA F 662 " --> pdb=" O GLN F 658 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'H' and resid 4 through 6 Processing sheet with id= B, first strand: chain 'H' and resid 33 through 36 Processing sheet with id= C, first strand: chain 'H' and resid 91 through 94 Processing sheet with id= D, first strand: chain 'L' and resid 6 through 8 Processing sheet with id= E, first strand: chain 'L' and resid 36 through 39 removed outlier: 3.644A pdb=" N UNK L 85 " --> pdb=" O UNK L 39 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 35 through 40 Processing sheet with id= G, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.715A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 53 through 55 Processing sheet with id= I, first strand: chain 'C' and resid 91 through 94 Processing sheet with id= J, first strand: chain 'C' and resid 130 through 133 Processing sheet with id= K, first strand: chain 'C' and resid 181 through 183 Processing sheet with id= L, first strand: chain 'C' and resid 200 through 203 Processing sheet with id= M, first strand: chain 'C' and resid 271 through 274 removed outlier: 6.251A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N ALA C 362 " --> pdb=" O PRO C 470 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 374 through 378 removed outlier: 4.001A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.454A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'A' and resid 35 through 40 Processing sheet with id= Q, first strand: chain 'A' and resid 45 through 47 Processing sheet with id= R, first strand: chain 'A' and resid 53 through 56 Processing sheet with id= S, first strand: chain 'A' and resid 91 through 94 Processing sheet with id= T, first strand: chain 'A' and resid 130 through 133 Processing sheet with id= U, first strand: chain 'A' and resid 181 through 183 Processing sheet with id= V, first strand: chain 'A' and resid 200 through 203 removed outlier: 3.555A pdb=" N ALA A 433 " --> pdb=" O ALA A 200 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'A' and resid 271 through 274 removed outlier: 6.417A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N ALA A 362 " --> pdb=" O PRO A 470 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'A' and resid 374 through 378 removed outlier: 4.094A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.419A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 35 through 40 Processing sheet with id= AA, first strand: chain 'E' and resid 45 through 47 Processing sheet with id= AB, first strand: chain 'E' and resid 53 through 55 Processing sheet with id= AC, first strand: chain 'E' and resid 91 through 94 Processing sheet with id= AD, first strand: chain 'E' and resid 130 through 133 Processing sheet with id= AE, first strand: chain 'E' and resid 181 through 183 Processing sheet with id= AF, first strand: chain 'E' and resid 200 through 203 Processing sheet with id= AG, first strand: chain 'E' and resid 271 through 274 removed outlier: 6.451A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N ALA E 362 " --> pdb=" O PRO E 470 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'E' and resid 414 through 417 removed outlier: 6.542A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'E' and resid 374 through 378 removed outlier: 4.312A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.486A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) 564 hydrogen bonds defined for protein. 1344 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.18 Time building geometry restraints manager: 7.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3687 1.32 - 1.46: 5040 1.46 - 1.60: 7295 1.60 - 1.74: 18 1.74 - 1.88: 134 Bond restraints: 16174 Sorted by residual: bond pdb=" CB HIS A 374 " pdb=" CG HIS A 374 " ideal model delta sigma weight residual 1.497 1.393 0.104 1.40e-02 5.10e+03 5.54e+01 bond pdb=" NE ARG A 503 " pdb=" CZ ARG A 503 " ideal model delta sigma weight residual 1.326 1.395 -0.069 1.10e-02 8.26e+03 3.98e+01 bond pdb=" NE ARG E 503 " pdb=" CZ ARG E 503 " ideal model delta sigma weight residual 1.326 1.394 -0.068 1.10e-02 8.26e+03 3.84e+01 bond pdb=" C5 NAG C 609 " pdb=" O5 NAG C 609 " ideal model delta sigma weight residual 1.435 1.503 -0.068 1.10e-02 8.26e+03 3.81e+01 bond pdb=" NE ARG C 503 " pdb=" CZ ARG C 503 " ideal model delta sigma weight residual 1.326 1.393 -0.067 1.10e-02 8.26e+03 3.72e+01 ... (remaining 16169 not shown) Histogram of bond angle deviations from ideal: 96.36 - 104.01: 182 104.01 - 111.66: 7613 111.66 - 119.32: 6516 119.32 - 126.97: 7455 126.97 - 134.62: 235 Bond angle restraints: 22001 Sorted by residual: angle pdb=" C GLU A 492 " pdb=" N PRO A 493 " pdb=" CA PRO A 493 " ideal model delta sigma weight residual 119.56 128.44 -8.88 1.02e+00 9.61e-01 7.58e+01 angle pdb=" C LEU F 523 " pdb=" N GLY F 524 " pdb=" CA GLY F 524 " ideal model delta sigma weight residual 120.10 128.29 -8.19 9.50e-01 1.11e+00 7.42e+01 angle pdb=" N ILE F 622 " pdb=" CA ILE F 622 " pdb=" C ILE F 622 " ideal model delta sigma weight residual 111.67 103.60 8.07 9.50e-01 1.11e+00 7.21e+01 angle pdb=" C ARG E 298 " pdb=" N PRO E 299 " pdb=" CA PRO E 299 " ideal model delta sigma weight residual 119.56 127.34 -7.78 1.01e+00 9.80e-01 5.93e+01 angle pdb=" C ARG C 298 " pdb=" N PRO C 299 " pdb=" CA PRO C 299 " ideal model delta sigma weight residual 119.56 127.32 -7.76 1.01e+00 9.80e-01 5.90e+01 ... (remaining 21996 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.20: 9299 17.20 - 34.40: 232 34.40 - 51.60: 75 51.60 - 68.80: 32 68.80 - 86.00: 12 Dihedral angle restraints: 9650 sinusoidal: 3994 harmonic: 5656 Sorted by residual: dihedral pdb=" CB CYS E 126 " pdb=" SG CYS E 126 " pdb=" SG CYS E 196 " pdb=" CB CYS E 196 " ideal model delta sinusoidal sigma weight residual 93.00 159.02 -66.02 1 1.00e+01 1.00e-02 5.70e+01 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 153.31 -60.31 1 1.00e+01 1.00e-02 4.85e+01 dihedral pdb=" CB CYS C 126 " pdb=" SG CYS C 126 " pdb=" SG CYS C 196 " pdb=" CB CYS C 196 " ideal model delta sinusoidal sigma weight residual 93.00 153.22 -60.22 1 1.00e+01 1.00e-02 4.83e+01 ... (remaining 9647 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.169: 2326 0.169 - 0.338: 348 0.338 - 0.507: 98 0.507 - 0.676: 1 0.676 - 0.845: 1 Chirality restraints: 2774 Sorted by residual: chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.42e+02 chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.23e+02 chirality pdb=" C1 NAG U 2 " pdb=" O4 NAG U 1 " pdb=" C2 NAG U 2 " pdb=" O5 NAG U 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.11e+02 ... (remaining 2771 not shown) Planarity restraints: 2776 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 610 " -0.349 2.00e-02 2.50e+03 3.01e-01 1.13e+03 pdb=" C7 NAG C 610 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG C 610 " -0.128 2.00e-02 2.50e+03 pdb=" N2 NAG C 610 " 0.535 2.00e-02 2.50e+03 pdb=" O7 NAG C 610 " -0.142 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 606 " -0.344 2.00e-02 2.50e+03 2.97e-01 1.10e+03 pdb=" C7 NAG E 606 " 0.082 2.00e-02 2.50e+03 pdb=" C8 NAG E 606 " -0.131 2.00e-02 2.50e+03 pdb=" N2 NAG E 606 " 0.529 2.00e-02 2.50e+03 pdb=" O7 NAG E 606 " -0.136 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 702 " 0.340 2.00e-02 2.50e+03 2.94e-01 1.08e+03 pdb=" C7 NAG B 702 " -0.079 2.00e-02 2.50e+03 pdb=" C8 NAG B 702 " 0.074 2.00e-02 2.50e+03 pdb=" N2 NAG B 702 " -0.520 2.00e-02 2.50e+03 pdb=" O7 NAG B 702 " 0.185 2.00e-02 2.50e+03 ... (remaining 2773 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1762 2.73 - 3.27: 15212 3.27 - 3.82: 24698 3.82 - 4.36: 31835 4.36 - 4.90: 49462 Nonbonded interactions: 122969 Sorted by model distance: nonbonded pdb=" O3 NAG A 614 " pdb=" O7 NAG A 614 " model vdw 2.188 2.440 nonbonded pdb=" O3 NAG I 2 " pdb=" O7 NAG I 2 " model vdw 2.294 2.440 nonbonded pdb=" OG1 THR C 240 " pdb=" O6 NAG C 602 " model vdw 2.413 2.440 nonbonded pdb=" C ASN A 195 " pdb=" OD1 ASN A 195 " model vdw 2.475 3.270 nonbonded pdb=" NZ LYS C 46 " pdb=" OD2 ASP D 632 " model vdw 2.491 2.520 ... (remaining 122964 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 33 through 57 or resid 66 through 397 or resid 414 through \ 503 or resid 601 through 611)) selection = (chain 'C' and (resid 33 through 57 or resid 66 through 185 or resid 189 through \ 503 or resid 601 through 611)) selection = (chain 'E' and (resid 33 through 503 or resid 601 through 611)) } ncs_group { reference = (chain 'B' and (resid 521 through 662 or resid 702)) selection = (chain 'D' and (resid 521 through 662 or resid 702)) selection = (chain 'F' and (resid 521 through 662 or resid 701)) } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'U' } ncs_group { reference = (chain 'H' and resid 16 through 114) selection = chain 'L' } ncs_group { reference = chain 'J' selection = chain 'P' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 105 5.16 5 C 9901 2.51 5 N 2711 2.21 5 O 3186 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.580 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: 11.210 Check model and map are aligned: 0.230 Process input model: 43.570 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Set scattering table: 0.160 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 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 : 0.020 0.128 16174 Z= 1.333 Angle : 1.644 10.118 22001 Z= 1.133 Chirality : 0.130 0.845 2774 Planarity : 0.018 0.301 2718 Dihedral : 10.058 85.998 5865 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.05 % 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: 1.02 (0.20), residues: 1709 helix: 0.16 (0.23), residues: 463 sheet: 1.04 (0.23), residues: 454 loop : 1.01 (0.22), residues: 792 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 528 time to evaluate : 1.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 528 average time/residue: 0.3046 time to fit residues: 228.2881 Evaluate side-chains 273 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 273 time to evaluate : 1.794 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 161 optimal weight: 6.9990 chunk 144 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 149 optimal weight: 0.8980 chunk 57 optimal weight: 6.9990 chunk 91 optimal weight: 0.8980 chunk 111 optimal weight: 0.8980 chunk 173 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 203 GLN D 551 GLN D 552 GLN ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 GLN E 216 HIS E 425 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 16174 Z= 0.242 Angle : 0.664 10.296 22001 Z= 0.368 Chirality : 0.047 0.386 2774 Planarity : 0.005 0.046 2718 Dihedral : 5.590 44.258 2570 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer Outliers : 0.06 % 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: 0.95 (0.20), residues: 1709 helix: 0.78 (0.24), residues: 440 sheet: 0.70 (0.23), residues: 408 loop : 0.71 (0.21), residues: 861 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 360 time to evaluate : 1.873 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 outliers start: 1 outliers final: 0 residues processed: 360 average time/residue: 0.2823 time to fit residues: 149.5025 Evaluate side-chains 230 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 230 time to evaluate : 1.775 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 96 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 144 optimal weight: 8.9990 chunk 118 optimal weight: 2.9990 chunk 47 optimal weight: 8.9990 chunk 173 optimal weight: 0.0270 chunk 187 optimal weight: 5.9990 chunk 154 optimal weight: 6.9990 chunk 172 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 139 optimal weight: 9.9990 overall best weight: 1.2040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 552 GLN D 563 GLN D 630 GLN A 85 HIS ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN E 249 HIS E 374 HIS ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 640 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 16174 Z= 0.217 Angle : 0.581 9.963 22001 Z= 0.312 Chirality : 0.045 0.293 2774 Planarity : 0.004 0.055 2718 Dihedral : 5.363 47.519 2570 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer Outliers : 0.06 % 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: 0.79 (0.20), residues: 1709 helix: 0.81 (0.25), residues: 442 sheet: 0.65 (0.24), residues: 417 loop : 0.47 (0.21), residues: 850 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 319 time to evaluate : 1.817 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 outliers start: 1 outliers final: 1 residues processed: 320 average time/residue: 0.2875 time to fit residues: 136.1091 Evaluate side-chains 224 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 223 time to evaluate : 1.708 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1353 time to fit residues: 2.4232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 171 optimal weight: 4.9990 chunk 130 optimal weight: 8.9990 chunk 90 optimal weight: 4.9990 chunk 19 optimal weight: 20.0000 chunk 82 optimal weight: 6.9990 chunk 116 optimal weight: 6.9990 chunk 174 optimal weight: 5.9990 chunk 184 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 165 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 552 GLN A 85 HIS A 302 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 GLN E 249 HIS ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.4695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.073 16174 Z= 0.455 Angle : 0.759 10.028 22001 Z= 0.404 Chirality : 0.050 0.323 2774 Planarity : 0.005 0.041 2718 Dihedral : 5.924 48.191 2570 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer Outliers : 0.00 % 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: 0.11 (0.19), residues: 1709 helix: 0.24 (0.24), residues: 450 sheet: 0.47 (0.24), residues: 430 loop : -0.11 (0.21), residues: 829 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 277 time to evaluate : 2.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 277 average time/residue: 0.2960 time to fit residues: 120.9126 Evaluate side-chains 197 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 1.806 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 153 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 137 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 157 optimal weight: 7.9990 chunk 127 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 94 optimal weight: 0.7980 chunk 165 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 203 GLN D 550 GLN D 552 GLN D 554 ASN D 651 ASN A 85 HIS ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN E 72 HIS ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.4905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 16174 Z= 0.223 Angle : 0.569 12.861 22001 Z= 0.304 Chirality : 0.045 0.298 2774 Planarity : 0.004 0.083 2718 Dihedral : 5.524 48.894 2570 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer Outliers : 0.06 % 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: 0.30 (0.20), residues: 1709 helix: 0.69 (0.25), residues: 437 sheet: 0.51 (0.24), residues: 410 loop : -0.11 (0.20), residues: 862 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 273 time to evaluate : 1.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 274 average time/residue: 0.2819 time to fit residues: 114.6832 Evaluate side-chains 200 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 1.741 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 62 optimal weight: 5.9990 chunk 166 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 108 optimal weight: 7.9990 chunk 45 optimal weight: 9.9990 chunk 184 optimal weight: 4.9990 chunk 153 optimal weight: 4.9990 chunk 85 optimal weight: 7.9990 chunk 15 optimal weight: 20.0000 chunk 61 optimal weight: 0.9980 chunk 97 optimal weight: 7.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 552 GLN D 658 GLN A 85 HIS ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN B 551 GLN B 552 GLN E 302 ASN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.5275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.059 16174 Z= 0.367 Angle : 0.658 9.467 22001 Z= 0.350 Chirality : 0.047 0.303 2774 Planarity : 0.004 0.049 2718 Dihedral : 5.747 48.992 2570 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer Outliers : 0.06 % 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: 0.05 (0.20), residues: 1709 helix: 0.54 (0.25), residues: 436 sheet: 0.31 (0.24), residues: 428 loop : -0.28 (0.21), residues: 845 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 258 time to evaluate : 1.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 259 average time/residue: 0.2855 time to fit residues: 109.8436 Evaluate side-chains 189 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 1.747 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 178 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 chunk 105 optimal weight: 3.9990 chunk 134 optimal weight: 0.0270 chunk 104 optimal weight: 5.9990 chunk 155 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 184 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 overall best weight: 1.4044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 550 GLN D 552 GLN ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 ASN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.5397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 16174 Z= 0.209 Angle : 0.546 6.189 22001 Z= 0.293 Chirality : 0.044 0.299 2774 Planarity : 0.004 0.042 2718 Dihedral : 5.521 49.536 2570 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer Outliers : 0.06 % 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: 0.18 (0.20), residues: 1709 helix: 0.74 (0.25), residues: 437 sheet: 0.37 (0.25), residues: 414 loop : -0.25 (0.21), residues: 858 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 259 time to evaluate : 1.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 260 average time/residue: 0.2929 time to fit residues: 112.2472 Evaluate side-chains 195 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 1.810 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 113 optimal weight: 0.0670 chunk 73 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 17 optimal weight: 20.0000 chunk 144 optimal weight: 1.9990 overall best weight: 1.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 170 GLN D 552 GLN ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.5527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 16174 Z= 0.209 Angle : 0.536 5.930 22001 Z= 0.290 Chirality : 0.044 0.309 2774 Planarity : 0.004 0.057 2718 Dihedral : 5.452 50.134 2570 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer Outliers : 0.00 % 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: 0.19 (0.20), residues: 1709 helix: 0.85 (0.26), residues: 435 sheet: 0.38 (0.25), residues: 415 loop : -0.29 (0.20), residues: 859 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 262 time to evaluate : 1.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 262 average time/residue: 0.2800 time to fit residues: 109.7163 Evaluate side-chains 201 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 1.708 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 167 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 171 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 134 optimal weight: 0.0770 chunk 52 optimal weight: 5.9990 chunk 155 optimal weight: 8.9990 chunk 162 optimal weight: 4.9990 chunk 170 optimal weight: 0.9990 overall best weight: 1.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 552 GLN ** D 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.5671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 16174 Z= 0.197 Angle : 0.531 8.417 22001 Z= 0.286 Chirality : 0.044 0.314 2774 Planarity : 0.004 0.042 2718 Dihedral : 5.412 52.134 2570 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer Outliers : 0.00 % 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: 0.19 (0.20), residues: 1709 helix: 1.00 (0.26), residues: 424 sheet: 0.35 (0.25), residues: 418 loop : -0.35 (0.20), residues: 867 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 263 time to evaluate : 1.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 263 average time/residue: 0.2788 time to fit residues: 109.7804 Evaluate side-chains 198 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 1.582 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 112 optimal weight: 0.9980 chunk 181 optimal weight: 0.0870 chunk 110 optimal weight: 0.7980 chunk 86 optimal weight: 0.4980 chunk 126 optimal weight: 3.9990 chunk 190 optimal weight: 6.9990 chunk 175 optimal weight: 5.9990 chunk 151 optimal weight: 1.9990 chunk 15 optimal weight: 20.0000 chunk 117 optimal weight: 0.0570 chunk 92 optimal weight: 2.9990 overall best weight: 0.4876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 552 GLN D 656 ASN A 328 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.5773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 16174 Z= 0.146 Angle : 0.518 11.946 22001 Z= 0.276 Chirality : 0.043 0.305 2774 Planarity : 0.004 0.055 2718 Dihedral : 5.284 51.941 2570 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer Outliers : 0.00 % 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: 0.28 (0.20), residues: 1709 helix: 1.00 (0.26), residues: 427 sheet: 0.49 (0.25), residues: 422 loop : -0.32 (0.20), residues: 860 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 283 time to evaluate : 1.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 283 average time/residue: 0.2881 time to fit residues: 121.7350 Evaluate side-chains 201 residues out of total 1548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 1.916 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 120 optimal weight: 0.9990 chunk 161 optimal weight: 10.0000 chunk 46 optimal weight: 0.6980 chunk 139 optimal weight: 8.9990 chunk 22 optimal weight: 0.8980 chunk 42 optimal weight: 9.9990 chunk 151 optimal weight: 0.7980 chunk 63 optimal weight: 9.9990 chunk 155 optimal weight: 5.9990 chunk 19 optimal weight: 20.0000 chunk 27 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 428 GLN D 550 GLN D 554 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.098836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.082526 restraints weight = 44624.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.084507 restraints weight = 28379.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.085879 restraints weight = 20785.350| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.5885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 16174 Z= 0.171 Angle : 0.523 8.294 22001 Z= 0.281 Chirality : 0.044 0.296 2774 Planarity : 0.004 0.059 2718 Dihedral : 5.274 52.408 2570 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer Outliers : 0.06 % 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: 0.22 (0.20), residues: 1709 helix: 0.82 (0.26), residues: 433 sheet: 0.56 (0.25), residues: 417 loop : -0.34 (0.20), residues: 859 =============================================================================== Job complete usr+sys time: 3139.24 seconds wall clock time: 58 minutes 1.84 seconds (3481.84 seconds total)