Starting phenix.real_space_refine (version: 1.21rc1) on Mon Aug 14 01:06:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sw7_40810/08_2023/8sw7_40810_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sw7_40810/08_2023/8sw7_40810.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sw7_40810/08_2023/8sw7_40810.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sw7_40810/08_2023/8sw7_40810.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sw7_40810/08_2023/8sw7_40810_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sw7_40810/08_2023/8sw7_40810_updated.pdb" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 102 5.16 5 C 9437 2.51 5 N 2600 2.21 5 O 2994 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 15133 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 3470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3470 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 20, 'TRANS': 419} Chain breaks: 3 Chain: "B" Number of atoms: 998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 998 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "C" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3424 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 20, 'TRANS': 412} Chain breaks: 4 Chain: "D" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 959 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "E" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 959 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "F" Number of atoms: 3365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3365 Classifications: {'peptide': 425} Link IDs: {'PTRANS': 18, 'TRANS': 406} Chain breaks: 5 Chain: "H" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 625 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 125} Link IDs: {'TRANS': 124} Unresolved non-hydrogen bonds: 250 Unresolved non-hydrogen angles: 375 Unresolved non-hydrogen dihedrals: 125 Planarities with less than four sites: {'UNK:plan-1': 125} Unresolved non-hydrogen planarities: 125 Chain: "L" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 530 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 106} Link IDs: {'TRANS': 105} Unresolved non-hydrogen bonds: 212 Unresolved non-hydrogen angles: 318 Unresolved non-hydrogen dihedrals: 106 Planarities with less than four sites: {'UNK:plan-1': 106} Unresolved non-hydrogen planarities: 106 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen 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: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen chiralities: 13 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen chiralities: 14 Time building chain proxies: 7.46, per 1000 atoms: 0.49 Number of scatterers: 15133 At special positions: 0 Unit cell: (128.875, 136.092, 120.627, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 102 16.00 O 2994 8.00 N 2600 7.00 C 9437 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.02 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.02 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.04 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.01 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 73 " distance=2.02 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.05 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.02 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS E 605 " distance=2.05 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS D 605 " - pdb=" SG CYS F 501 " distance=2.10 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 73 " distance=2.03 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.04 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.02 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.06 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 133 " " NAG A 603 " - " ASN A 137 " " NAG A 604 " - " ASN A 156 " " NAG A 605 " - " ASN A 160 " " NAG A 606 " - " ASN A 197 " " NAG A 607 " - " ASN A 234 " " NAG A 608 " - " ASN A 241 " " NAG A 609 " - " ASN A 276 " " NAG A 610 " - " ASN A 289 " " NAG A 611 " - " ASN A 301 " " NAG A 612 " - " ASN A 332 " " NAG A 613 " - " ASN A 392 " " NAG A 614 " - " ASN A 448 " " NAG A 615 " - " ASN A 295 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 618 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 133 " " NAG C 603 " - " ASN C 156 " " NAG C 604 " - " ASN C 160 " " NAG C 605 " - " ASN C 234 " " NAG C 606 " - " ASN C 241 " " NAG C 607 " - " ASN C 289 " " NAG C 608 " - " ASN C 295 " " NAG C 609 " - " ASN C 301 " " NAG C 610 " - " ASN C 332 " " NAG C 611 " - " ASN C 392 " " NAG C 612 " - " ASN C 448 " " NAG C 613 " - " ASN C 386 " " NAG D 701 " - " ASN D 611 " " NAG D 702 " - " ASN D 637 " " NAG E 701 " - " ASN E 611 " " NAG E 702 " - " ASN E 618 " " NAG E 703 " - " ASN E 637 " " NAG F 601 " - " ASN F 88 " " NAG F 602 " - " ASN F 133 " " NAG F 603 " - " ASN F 156 " " NAG F 604 " - " ASN F 160 " " NAG F 605 " - " ASN F 234 " " NAG F 606 " - " ASN F 241 " " NAG F 607 " - " ASN F 276 " " NAG F 608 " - " ASN F 289 " " NAG F 609 " - " ASN F 295 " " NAG F 610 " - " ASN F 301 " " NAG F 611 " - " ASN F 332 " " NAG F 612 " - " ASN F 386 " " NAG F 613 " - " ASN F 392 " " NAG F 614 " - " ASN F 448 " " NAG G 1 " - " ASN A 262 " " NAG I 1 " - " ASN C 262 " " NAG J 1 " - " ASN F 262 " Time building additional restraints: 5.80 Conformation dependent library (CDL) restraints added in 1.9 seconds 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3578 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 39 helices and 37 sheets defined 24.8% alpha, 26.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.46 Creating SS restraints... Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 123 through 125 No H-bonds generated for 'chain 'A' and resid 123 through 125' Processing helix chain 'A' and resid 140 through 150 No H-bonds generated for 'chain 'A' and resid 140 through 150' Processing helix chain 'A' and resid 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 335 through 353 removed outlier: 4.123A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 372 No H-bonds generated for 'chain 'A' and resid 369 through 372' Processing helix chain 'A' and resid 475 through 485 removed outlier: 3.708A pdb=" N ARG A 480 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N SER A 481 " --> pdb=" O ASN A 478 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N TYR A 484 " --> pdb=" O SER A 481 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LYS A 485 " --> pdb=" O GLU A 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 527 removed outlier: 4.383A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 524 through 527' Processing helix chain 'B' and resid 530 through 543 removed outlier: 5.117A pdb=" N MET B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N THR B 536 " --> pdb=" O ALA B 532 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU B 537 " --> pdb=" O ALA B 533 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N THR B 538 " --> pdb=" O SER B 534 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N VAL B 539 " --> pdb=" O MET B 535 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 595 Processing helix chain 'B' and resid 612 through 614 No H-bonds generated for 'chain 'B' and resid 612 through 614' Processing helix chain 'B' and resid 620 through 623 No H-bonds generated for 'chain 'B' and resid 620 through 623' Processing helix chain 'B' and resid 628 through 634 Processing helix chain 'B' and resid 636 through 660 removed outlier: 5.295A pdb=" N GLN B 640 " --> pdb=" O ASN B 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 97 No H-bonds generated for 'chain 'C' and resid 95 through 97' Processing helix chain 'C' and resid 99 through 115 Processing helix chain 'C' and resid 123 through 125 No H-bonds generated for 'chain 'C' and resid 123 through 125' Processing helix chain 'C' and resid 178 through 180 No H-bonds generated for 'chain 'C' and resid 178 through 180' Processing helix chain 'C' and resid 335 through 352 removed outlier: 4.206A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 372 No H-bonds generated for 'chain 'C' and resid 369 through 372' Processing helix chain 'C' and resid 476 through 485 removed outlier: 4.489A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LYS C 485 " --> pdb=" O SER C 481 " (cutoff:3.500A) Processing helix chain 'D' and resid 530 through 541 removed outlier: 5.111A pdb=" N MET D 535 " --> pdb=" O GLY D 531 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N THR D 536 " --> pdb=" O ALA D 532 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LEU D 537 " --> pdb=" O ALA D 533 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N THR D 538 " --> pdb=" O SER D 534 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N VAL D 539 " --> pdb=" O MET D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 595 Processing helix chain 'D' and resid 619 through 624 Processing helix chain 'D' and resid 628 through 634 removed outlier: 3.529A pdb=" N LYS D 633 " --> pdb=" O LEU D 629 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU D 634 " --> pdb=" O GLN D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 662 removed outlier: 5.168A pdb=" N GLN D 640 " --> pdb=" O ASN D 637 " (cutoff:3.500A) Processing helix chain 'E' and resid 524 through 527 removed outlier: 4.178A pdb=" N GLY E 527 " --> pdb=" O GLY E 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 524 through 527' Processing helix chain 'E' and resid 533 through 542 removed outlier: 3.509A pdb=" N LEU E 537 " --> pdb=" O SER E 534 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N THR E 538 " --> pdb=" O MET E 535 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA E 541 " --> pdb=" O THR E 538 " (cutoff:3.500A) Processing helix chain 'E' and resid 573 through 595 Processing helix chain 'E' and resid 619 through 622 No H-bonds generated for 'chain 'E' and resid 619 through 622' Processing helix chain 'E' and resid 628 through 663 removed outlier: 5.855A pdb=" N ASN E 637 " --> pdb=" O LYS E 633 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N TYR E 638 " --> pdb=" O GLU E 634 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N THR E 639 " --> pdb=" O ILE E 635 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N GLN E 640 " --> pdb=" O SER E 636 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N ILE E 641 " --> pdb=" O ASN E 637 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU E 663 " --> pdb=" O ASP E 659 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 117 Processing helix chain 'F' and resid 164 through 166 No H-bonds generated for 'chain 'F' and resid 164 through 166' Processing helix chain 'F' and resid 178 through 180 No H-bonds generated for 'chain 'F' and resid 178 through 180' Processing helix chain 'F' and resid 335 through 352 removed outlier: 4.073A pdb=" N LYS F 351 " --> pdb=" O LYS F 347 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N HIS F 352 " --> pdb=" O GLN F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 372 No H-bonds generated for 'chain 'F' and resid 369 through 372' Processing helix chain 'F' and resid 477 through 485 removed outlier: 4.239A pdb=" N GLU F 482 " --> pdb=" O ASN F 478 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LYS F 485 " --> pdb=" O SER F 481 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing helix chain 'H' and resid 65 through 67 No H-bonds generated for 'chain 'H' and resid 65 through 67' Processing sheet with id= A, first strand: chain 'A' and resid 35 through 40 Processing sheet with id= B, first strand: chain 'A' and resid 45 through 47 Processing sheet with id= C, first strand: chain 'A' and resid 53 through 55 Processing sheet with id= D, first strand: chain 'A' and resid 91 through 94 Processing sheet with id= E, first strand: chain 'A' and resid 130 through 133 Processing sheet with id= F, first strand: chain 'A' and resid 181 through 183 Processing sheet with id= G, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.576A pdb=" N ALA A 433 " --> pdb=" O THR A 202 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'A' and resid 271 through 274 removed outlier: 6.904A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 443 through 449 removed outlier: 6.631A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 465 through 469 removed outlier: 6.372A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.108A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 35 through 40 Processing sheet with id= M, first strand: chain 'C' and resid 45 through 47 Processing sheet with id= N, first strand: chain 'C' and resid 53 through 55 Processing sheet with id= O, first strand: chain 'C' and resid 91 through 94 Processing sheet with id= P, first strand: chain 'C' and resid 172 through 177 Processing sheet with id= Q, first strand: chain 'C' and resid 201 through 203 removed outlier: 6.581A pdb=" N ALA C 433 " --> pdb=" O THR C 202 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.369A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N ALA C 362 " --> pdb=" O PRO C 470 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 374 through 378 removed outlier: 3.986A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.417A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 35 through 40 Processing sheet with id= V, first strand: chain 'F' and resid 45 through 47 removed outlier: 4.653A pdb=" N VAL F 242 " --> pdb=" O LEU F 86 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 53 through 55 Processing sheet with id= X, first strand: chain 'F' and resid 91 through 94 removed outlier: 3.877A pdb=" N GLU F 91 " --> pdb=" O CYS F 239 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'F' and resid 131 through 133 Processing sheet with id= Z, first strand: chain 'F' and resid 181 through 183 Processing sheet with id= AA, first strand: chain 'F' and resid 201 through 203 removed outlier: 6.518A pdb=" N ALA F 433 " --> pdb=" O THR F 202 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'F' and resid 271 through 273 removed outlier: 6.611A pdb=" N LEU F 260 " --> pdb=" O THR F 450 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 443 through 449 removed outlier: 7.511A pdb=" N GLN F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N SER F 334 " --> pdb=" O GLN F 293 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA F 329 " --> pdb=" O CYS F 418 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 382 through 384 removed outlier: 4.030A pdb=" N PHE F 382 " --> pdb=" O LYS F 421 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'F' and resid 304 through 312 removed outlier: 6.434A pdb=" N GLN F 315 " --> pdb=" O ILE F 309 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'H' and resid 18 through 21 Processing sheet with id= AG, first strand: chain 'H' and resid 119 through 121 removed outlier: 4.227A pdb=" N UNK H 34 " --> pdb=" O UNK H 51 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N UNK H 38 " --> pdb=" O UNK H 47 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N UNK H 47 " --> pdb=" O UNK H 38 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N UNK H 40 " --> pdb=" O UNK H 45 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N UNK H 45 " --> pdb=" O UNK H 40 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'L' and resid 4 through 6 Processing sheet with id= AI, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.638A pdb=" N UNK L 104 " --> pdb=" O UNK L 11 " (cutoff:3.500A) No H-bonds generated for sheet with id= AI Processing sheet with id= AJ, first strand: chain 'L' and resid 88 through 91 removed outlier: 5.369A pdb=" N UNK L 37 " --> pdb=" O UNK L 46 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N UNK L 46 " --> pdb=" O UNK L 37 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'H' and resid 97 through 99 removed outlier: 3.531A pdb=" N UNK H 114 " --> pdb=" O UNK H 98 " (cutoff:3.500A) 508 hydrogen bonds defined for protein. 1251 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.91 Time building geometry restraints manager: 6.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.33: 3792 1.33 - 1.48: 5118 1.48 - 1.63: 6341 1.63 - 1.78: 52 1.78 - 1.94: 86 Bond restraints: 15389 Sorted by residual: bond pdb=" NE ARG F 504 " pdb=" CZ ARG F 504 " ideal model delta sigma weight residual 1.326 1.406 -0.080 1.10e-02 8.26e+03 5.24e+01 bond pdb=" NE ARG A 504 " pdb=" CZ ARG A 504 " ideal model delta sigma weight residual 1.326 1.399 -0.073 1.10e-02 8.26e+03 4.42e+01 bond pdb=" CD2 TRP E 571 " pdb=" CE3 TRP E 571 " ideal model delta sigma weight residual 1.398 1.504 -0.106 1.60e-02 3.91e+03 4.36e+01 bond pdb=" CD2 TRP D 571 " pdb=" CE3 TRP D 571 " ideal model delta sigma weight residual 1.398 1.500 -0.102 1.60e-02 3.91e+03 4.07e+01 bond pdb=" CZ2 TRP E 571 " pdb=" CH2 TRP E 571 " ideal model delta sigma weight residual 1.368 1.489 -0.121 1.90e-02 2.77e+03 4.03e+01 ... (remaining 15384 not shown) Histogram of bond angle deviations from ideal: 96.98 - 104.42: 217 104.42 - 111.87: 7244 111.87 - 119.32: 5998 119.32 - 126.76: 7204 126.76 - 134.21: 263 Bond angle restraints: 20926 Sorted by residual: angle pdb=" N PRO A 437 " pdb=" CA PRO A 437 " pdb=" C PRO A 437 " ideal model delta sigma weight residual 110.58 100.83 9.75 1.07e+00 8.73e-01 8.30e+01 angle pdb=" N ARG F 476 " pdb=" CA ARG F 476 " pdb=" C ARG F 476 " ideal model delta sigma weight residual 114.04 102.96 11.08 1.24e+00 6.50e-01 7.99e+01 angle pdb=" C ARG F 298 " pdb=" N PRO F 299 " pdb=" CA PRO F 299 " ideal model delta sigma weight residual 119.56 127.25 -7.69 1.01e+00 9.80e-01 5.79e+01 angle pdb=" C ARG A 298 " pdb=" N PRO A 299 " pdb=" CA PRO A 299 " ideal model delta sigma weight residual 119.56 127.19 -7.63 1.01e+00 9.80e-01 5.71e+01 angle pdb=" N PRO F 437 " pdb=" CA PRO F 437 " pdb=" C PRO F 437 " ideal model delta sigma weight residual 110.58 102.50 8.08 1.07e+00 8.73e-01 5.71e+01 ... (remaining 20921 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 8492 17.50 - 35.00: 215 35.00 - 52.50: 76 52.50 - 70.00: 23 70.00 - 87.50: 11 Dihedral angle restraints: 8817 sinusoidal: 3325 harmonic: 5492 Sorted by residual: dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 174.83 -81.83 1 1.00e+01 1.00e-02 8.24e+01 dihedral pdb=" CB CYS F 126 " pdb=" SG CYS F 126 " pdb=" SG CYS F 196 " pdb=" CB CYS F 196 " ideal model delta sinusoidal sigma weight residual 93.00 140.08 -47.08 1 1.00e+01 1.00e-02 3.06e+01 dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual -86.00 -129.29 43.29 1 1.00e+01 1.00e-02 2.61e+01 ... (remaining 8814 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 1757 0.102 - 0.203: 526 0.203 - 0.304: 170 0.304 - 0.406: 97 0.406 - 0.507: 34 Chirality restraints: 2584 Sorted by residual: chirality pdb=" C1 BMA I 3 " pdb=" O4 NAG I 2 " pdb=" C2 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.52e+02 chirality pdb=" C1 BMA J 3 " pdb=" O4 NAG J 2 " pdb=" C2 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 1.04e+02 chirality pdb=" C1 BMA G 3 " pdb=" O4 NAG G 2 " pdb=" C2 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.84e+01 ... (remaining 2581 not shown) Planarity restraints: 2665 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN D 611 " -0.099 2.00e-02 2.50e+03 1.04e-01 1.35e+02 pdb=" CG ASN D 611 " 0.041 2.00e-02 2.50e+03 pdb=" OD1 ASN D 611 " 0.022 2.00e-02 2.50e+03 pdb=" ND2 ASN D 611 " 0.161 2.00e-02 2.50e+03 pdb=" C1 NAG D 701 " -0.126 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 234 " -0.095 2.00e-02 2.50e+03 9.81e-02 1.20e+02 pdb=" CG ASN A 234 " 0.045 2.00e-02 2.50e+03 pdb=" OD1 ASN A 234 " 0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN A 234 " 0.151 2.00e-02 2.50e+03 pdb=" C1 NAG A 607 " -0.119 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 133 " 0.076 2.00e-02 2.50e+03 7.89e-02 7.77e+01 pdb=" CG ASN C 133 " -0.036 2.00e-02 2.50e+03 pdb=" OD1 ASN C 133 " -0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN C 133 " -0.121 2.00e-02 2.50e+03 pdb=" C1 NAG C 602 " 0.096 2.00e-02 2.50e+03 ... (remaining 2662 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1886 2.73 - 3.27: 14070 3.27 - 3.82: 23445 3.82 - 4.36: 29646 4.36 - 4.90: 47937 Nonbonded interactions: 116984 Sorted by model distance: nonbonded pdb=" OG1 THR F 37 " pdb=" OG1 THR F 499 " model vdw 2.188 2.440 nonbonded pdb=" N UNK H 51 " pdb=" N UNK H 52 " model vdw 2.394 2.560 nonbonded pdb=" NZ LYS C 231 " pdb=" OE1 GLU C 267 " model vdw 2.418 2.520 nonbonded pdb=" N LEU F 125 " pdb=" O LEU F 125 " model vdw 2.419 2.496 nonbonded pdb=" N VAL F 127 " pdb=" O VAL F 127 " model vdw 2.423 2.496 ... (remaining 116979 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 32 through 77 or resid 82 through 392 or resid 412 through \ 457 or resid 463 through 503 or resid 603 through 614)) selection = (chain 'C' and (resid 32 through 77 or resid 82 through 392 or resid 412 through \ 503 or resid 601 through 612)) selection = (chain 'F' and (resid 32 through 503 or resid 603 through 614)) } ncs_group { reference = (chain 'B' and (resid 522 through 664 or resid 701 through 702)) selection = chain 'D' selection = (chain 'E' and (resid 522 through 664 or resid 701 through 702)) } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.800 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: 0.240 Set scattering table: 0.140 Process input model: 38.420 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.022 0.145 15389 Z= 1.396 Angle : 1.718 11.084 20926 Z= 1.109 Chirality : 0.133 0.507 2584 Planarity : 0.009 0.052 2613 Dihedral : 10.034 87.497 5140 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 1.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.16 % Favored : 97.78 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.20), residues: 1622 helix: 0.55 (0.26), residues: 376 sheet: 1.10 (0.25), residues: 398 loop : 0.33 (0.22), residues: 848 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 599 time to evaluate : 1.550 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: 2 outliers final: 0 residues processed: 601 average time/residue: 0.2865 time to fit residues: 245.4190 Evaluate side-chains 366 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 366 time to evaluate : 1.542 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 157 optimal weight: 0.9990 chunk 141 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 146 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 109 optimal weight: 0.6980 chunk 169 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS A 103 GLN A 114 GLN A 195 ASN A 203 GLN A 302 ASN A 422 GLN A 425 ASN C 130 GLN C 287 GLN D 607 ASN E 575 GLN E 591 GLN F 203 GLN F 283 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 15389 Z= 0.248 Angle : 0.723 16.420 20926 Z= 0.369 Chirality : 0.047 0.244 2584 Planarity : 0.005 0.082 2613 Dihedral : 5.252 52.313 1994 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer Outliers : 3.11 % 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 (0.21), residues: 1622 helix: 0.84 (0.27), residues: 369 sheet: 0.61 (0.24), residues: 436 loop : -0.25 (0.22), residues: 817 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 430 time to evaluate : 1.498 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: 46 outliers final: 29 residues processed: 452 average time/residue: 0.2545 time to fit residues: 170.4789 Evaluate side-chains 401 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 372 time to evaluate : 1.484 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.1378 time to fit residues: 9.4480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 94 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 170 optimal weight: 6.9990 chunk 183 optimal weight: 10.0000 chunk 151 optimal weight: 3.9990 chunk 168 optimal weight: 9.9990 chunk 57 optimal weight: 0.0980 chunk 136 optimal weight: 0.7980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN A 258 GLN A 422 GLN A 478 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.072 15389 Z= 0.303 Angle : 0.679 17.113 20926 Z= 0.347 Chirality : 0.047 0.264 2584 Planarity : 0.004 0.045 2613 Dihedral : 5.020 49.174 1994 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer Outliers : 2.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.21), residues: 1622 helix: 0.87 (0.28), residues: 356 sheet: 0.27 (0.23), residues: 469 loop : -0.45 (0.22), residues: 797 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 399 time to evaluate : 1.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 29 residues processed: 427 average time/residue: 0.2647 time to fit residues: 167.2863 Evaluate side-chains 389 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 360 time to evaluate : 1.594 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 29 outliers final: 1 residues processed: 29 average time/residue: 0.1339 time to fit residues: 9.5705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 168 optimal weight: 10.0000 chunk 127 optimal weight: 0.8980 chunk 88 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 81 optimal weight: 8.9990 chunk 114 optimal weight: 0.9980 chunk 170 optimal weight: 5.9990 chunk 180 optimal weight: 10.0000 chunk 89 optimal weight: 0.8980 chunk 161 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN C 33 ASN C 287 GLN F 283 ASN F 478 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 15389 Z= 0.201 Angle : 0.600 16.114 20926 Z= 0.305 Chirality : 0.044 0.182 2584 Planarity : 0.004 0.036 2613 Dihedral : 4.776 40.467 1994 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer Outliers : 1.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.20), residues: 1622 helix: 1.00 (0.28), residues: 355 sheet: 0.17 (0.24), residues: 452 loop : -0.63 (0.21), residues: 815 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 367 time to evaluate : 1.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 19 residues processed: 380 average time/residue: 0.2642 time to fit residues: 148.2179 Evaluate side-chains 367 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 348 time to evaluate : 1.560 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 19 outliers final: 1 residues processed: 19 average time/residue: 0.1330 time to fit residues: 6.9308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 150 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 134 optimal weight: 0.9990 chunk 74 optimal weight: 7.9990 chunk 154 optimal weight: 3.9990 chunk 124 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 162 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS A 478 ASN B 616 ASN ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.4446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.057 15389 Z= 0.425 Angle : 0.740 15.635 20926 Z= 0.371 Chirality : 0.048 0.211 2584 Planarity : 0.005 0.048 2613 Dihedral : 5.110 38.025 1994 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer Outliers : 3.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.20), residues: 1622 helix: 0.83 (0.28), residues: 349 sheet: -0.18 (0.23), residues: 453 loop : -0.97 (0.21), residues: 820 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 359 time to evaluate : 1.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 33 residues processed: 379 average time/residue: 0.2595 time to fit residues: 146.1274 Evaluate side-chains 368 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 335 time to evaluate : 1.553 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 33 outliers final: 1 residues processed: 33 average time/residue: 0.1690 time to fit residues: 11.6711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 60 optimal weight: 0.9980 chunk 162 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 106 optimal weight: 0.0770 chunk 44 optimal weight: 1.9990 chunk 180 optimal weight: 9.9990 chunk 150 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 616 ASN C 195 ASN F 85 HIS F 203 GLN F 283 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.4638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 15389 Z= 0.204 Angle : 0.616 15.191 20926 Z= 0.311 Chirality : 0.044 0.233 2584 Planarity : 0.004 0.038 2613 Dihedral : 4.815 35.219 1994 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer Outliers : 1.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.20), residues: 1622 helix: 0.87 (0.29), residues: 362 sheet: -0.10 (0.24), residues: 440 loop : -1.00 (0.21), residues: 820 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 377 time to evaluate : 1.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 14 residues processed: 384 average time/residue: 0.2780 time to fit residues: 156.2905 Evaluate side-chains 362 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 348 time to evaluate : 1.537 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 14 outliers final: 1 residues processed: 14 average time/residue: 0.1415 time to fit residues: 5.8185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 174 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 152 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 chunk 180 optimal weight: 10.0000 chunk 112 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 83 optimal weight: 6.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN B 616 ASN C 195 ASN F 283 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.4878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 15389 Z= 0.281 Angle : 0.631 14.873 20926 Z= 0.318 Chirality : 0.045 0.217 2584 Planarity : 0.004 0.054 2613 Dihedral : 4.803 33.739 1994 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer Outliers : 1.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.20), residues: 1622 helix: 0.88 (0.29), residues: 356 sheet: -0.32 (0.24), residues: 442 loop : -1.06 (0.21), residues: 824 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 352 time to evaluate : 1.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 20 residues processed: 359 average time/residue: 0.2615 time to fit residues: 139.1968 Evaluate side-chains 365 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 345 time to evaluate : 1.664 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 20 outliers final: 1 residues processed: 20 average time/residue: 0.1415 time to fit residues: 7.5127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 111 optimal weight: 0.9980 chunk 71 optimal weight: 6.9990 chunk 107 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 chunk 122 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 141 optimal weight: 10.0000 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN ** C 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 283 ASN F 478 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.4998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 15389 Z= 0.192 Angle : 0.583 14.556 20926 Z= 0.293 Chirality : 0.044 0.204 2584 Planarity : 0.004 0.045 2613 Dihedral : 4.618 37.979 1994 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer Outliers : 1.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.21), residues: 1622 helix: 0.94 (0.29), residues: 362 sheet: -0.19 (0.25), residues: 424 loop : -1.10 (0.21), residues: 836 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 369 time to evaluate : 1.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 13 residues processed: 375 average time/residue: 0.2665 time to fit residues: 148.3909 Evaluate side-chains 367 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 354 time to evaluate : 1.569 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 13 outliers final: 1 residues processed: 13 average time/residue: 0.1329 time to fit residues: 5.4732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 163 optimal weight: 0.9980 chunk 172 optimal weight: 10.0000 chunk 157 optimal weight: 3.9990 chunk 167 optimal weight: 10.0000 chunk 101 optimal weight: 6.9990 chunk 73 optimal weight: 0.4980 chunk 131 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 151 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN C 348 GLN ** C 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 283 ASN F 425 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.5121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 15389 Z= 0.217 Angle : 0.593 14.259 20926 Z= 0.299 Chirality : 0.044 0.191 2584 Planarity : 0.004 0.034 2613 Dihedral : 4.607 38.168 1994 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer Outliers : 1.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.21), residues: 1622 helix: 0.93 (0.29), residues: 362 sheet: -0.23 (0.25), residues: 424 loop : -1.15 (0.21), residues: 836 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 360 time to evaluate : 1.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 12 residues processed: 366 average time/residue: 0.2652 time to fit residues: 144.0807 Evaluate side-chains 360 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 348 time to evaluate : 1.626 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 12 outliers final: 1 residues processed: 12 average time/residue: 0.1423 time to fit residues: 5.3967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 177 optimal weight: 10.0000 chunk 108 optimal weight: 0.5980 chunk 84 optimal weight: 7.9990 chunk 123 optimal weight: 3.9990 chunk 186 optimal weight: 10.0000 chunk 171 optimal weight: 8.9990 chunk 148 optimal weight: 0.9980 chunk 15 optimal weight: 7.9990 chunk 114 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 117 optimal weight: 7.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 ASN F 283 ASN F 478 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.5243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.061 15389 Z= 0.468 Angle : 0.750 14.202 20926 Z= 0.375 Chirality : 0.049 0.222 2584 Planarity : 0.005 0.052 2613 Dihedral : 5.074 38.429 1994 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer Outliers : 0.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.20), residues: 1622 helix: 0.65 (0.28), residues: 360 sheet: -0.37 (0.25), residues: 403 loop : -1.41 (0.20), residues: 859 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 351 time to evaluate : 1.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 9 residues processed: 356 average time/residue: 0.2660 time to fit residues: 141.3534 Evaluate side-chains 348 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 339 time to evaluate : 1.599 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 9 average time/residue: 0.1781 time to fit residues: 5.0219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 158 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 148 optimal weight: 0.0970 chunk 62 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 chunk 18 optimal weight: 0.4980 chunk 27 optimal weight: 0.9990 chunk 130 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 652 GLN F 283 ASN F 478 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.162360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.137580 restraints weight = 23236.837| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 3.38 r_work: 0.3554 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.5396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 15389 Z= 0.172 Angle : 0.611 14.586 20926 Z= 0.306 Chirality : 0.044 0.207 2584 Planarity : 0.004 0.037 2613 Dihedral : 4.664 37.700 1994 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer Outliers : 0.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.21), residues: 1622 helix: 0.89 (0.29), residues: 362 sheet: -0.17 (0.25), residues: 413 loop : -1.31 (0.20), residues: 847 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3599.97 seconds wall clock time: 65 minutes 58.32 seconds (3958.32 seconds total)