Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 13:26:50 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7moa_23922/04_2023/7moa_23922_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7moa_23922/04_2023/7moa_23922.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7moa_23922/04_2023/7moa_23922.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7moa_23922/04_2023/7moa_23922.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7moa_23922/04_2023/7moa_23922_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7moa_23922/04_2023/7moa_23922_updated.pdb" } resolution = 4.9 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= 0.002 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 128 5.16 5 C 7830 2.51 5 N 2163 2.21 5 O 2390 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 54": "OD1" <-> "OD2" Residue "D TYR 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 12511 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2047 Classifications: {'peptide': 254} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 236} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "E" Number of atoms: 5324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5324 Classifications: {'peptide': 688} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PCIS': 2, 'PTRANS': 31, 'TRANS': 654} Chain breaks: 4 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 87 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'HIS:plan': 1, 'ARG:plan': 4, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 67 Chain: "D" Number of atoms: 4946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 638, 4946 Classifications: {'peptide': 638} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 597} Chain breaks: 5 Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 227 Unresolved non-hydrogen dihedrals: 167 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 133 Chain: "F" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 97 Unusual residues: {'IDS': 3, 'SGN': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 8 Chain: "J" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 97 Unusual residues: {'IDS': 3, 'SGN': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 6.89, per 1000 atoms: 0.55 Number of scatterers: 12511 At special positions: 0 Unit cell: (133.92, 141.48, 104.76, 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 128 16.00 O 2390 8.00 N 2163 7.00 C 7830 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 70 " - pdb=" SG CYS A 96 " distance=2.02 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS A 84 " distance=2.03 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 206 " distance=2.03 Simple disulfide: pdb=" SG CYS A 149 " - pdb=" SG CYS A 189 " distance=2.02 Simple disulfide: pdb=" SG CYS A 177 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 211 " - pdb=" SG CYS A 288 " distance=2.03 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 271 " distance=2.03 Simple disulfide: pdb=" SG CYS A 260 " - pdb=" SG CYS A 283 " distance=2.03 Simple disulfide: pdb=" SG CYS E 26 " - pdb=" SG CYS E 584 " distance=2.03 Simple disulfide: pdb=" SG CYS E 95 " - pdb=" SG CYS E 101 " distance=2.03 Simple disulfide: pdb=" SG CYS E 98 " - pdb=" SG CYS E 160 " distance=2.03 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.04 Simple disulfide: pdb=" SG CYS E 172 " - pdb=" SG CYS E 175 " distance=2.03 Simple disulfide: pdb=" SG CYS E 282 " - pdb=" SG CYS E 409 " distance=2.02 Simple disulfide: pdb=" SG CYS E 298 " - pdb=" SG CYS E 363 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 397 " distance=2.04 Simple disulfide: pdb=" SG CYS E 520 " - pdb=" SG CYS E 538 " distance=2.03 Simple disulfide: pdb=" SG CYS E 526 " - pdb=" SG CYS E 561 " distance=2.02 Simple disulfide: pdb=" SG CYS E 529 " - pdb=" SG CYS E 545 " distance=2.03 Simple disulfide: pdb=" SG CYS E 541 " - pdb=" SG CYS E 551 " distance=2.04 Simple disulfide: pdb=" SG CYS E 610 " - pdb=" SG CYS E 624 " distance=2.03 Simple disulfide: pdb=" SG CYS E 697 " - pdb=" SG CYS E 709 " distance=2.03 Simple disulfide: pdb=" SG CYS D 70 " - pdb=" SG CYS D 96 " distance=2.01 Simple disulfide: pdb=" SG CYS D 74 " - pdb=" SG CYS D 84 " distance=2.03 Simple disulfide: pdb=" SG CYS D 128 " - pdb=" SG CYS D 206 " distance=2.03 Simple disulfide: pdb=" SG CYS D 149 " - pdb=" SG CYS D 189 " distance=2.03 Simple disulfide: pdb=" SG CYS D 177 " - pdb=" SG CYS D 201 " distance=2.03 Simple disulfide: pdb=" SG CYS D 211 " - pdb=" SG CYS D 288 " distance=2.04 Simple disulfide: pdb=" SG CYS D 232 " - pdb=" SG CYS D 271 " distance=2.03 Simple disulfide: pdb=" SG CYS D 260 " - pdb=" SG CYS D 283 " distance=2.02 Simple disulfide: pdb=" SG CYS D 305 " - pdb=" SG CYS D 383 " distance=2.03 Simple disulfide: pdb=" SG CYS D 326 " - pdb=" SG CYS D 365 " distance=2.02 Simple disulfide: pdb=" SG CYS D 354 " - pdb=" SG CYS D 377 " distance=2.04 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 469 " distance=2.03 Simple disulfide: pdb=" SG CYS D 412 " - pdb=" SG CYS D 452 " distance=2.02 Simple disulfide: pdb=" SG CYS D 440 " - pdb=" SG CYS D 464 " distance=2.04 Simple disulfide: pdb=" SG CYS D 519 " - pdb=" SG CYS D 535 " distance=2.02 Simple disulfide: pdb=" SG CYS D 612 " - pdb=" SG CYS D 679 " distance=2.05 Simple disulfide: pdb=" SG CYS D 642 " - pdb=" SG CYS D 658 " distance=2.02 Simple disulfide: pdb=" SG CYS D 669 " - pdb=" SG CYS D 697 " 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 ALPHA1-4 " IDS F 2 " - " SGN F 3 " " IDS F 4 " - " SGN F 5 " " IDS J 2 " - " SGN J 3 " " IDS J 4 " - " SGN J 5 " BETA1-4 " SGN F 1 " - " IDS F 2 " ~> Even though IDS is an alpha isomer, a beta linkage is required... " SGN F 3 " - " IDS F 4 " " SGN F 5 " - " IDS F 6 " " SGN J 1 " - " IDS J 2 " " SGN J 3 " - " IDS J 4 " " SGN J 5 " - " IDS J 6 " Time building additional restraints: 5.77 Conformation dependent library (CDL) restraints added in 1.9 seconds 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2942 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 23 helices and 27 sheets defined 8.7% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'A' and resid 38 through 40 No H-bonds generated for 'chain 'A' and resid 38 through 40' Processing helix chain 'A' and resid 67 through 75 Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 162 through 166 removed outlier: 3.987A pdb=" N SER A 165 " --> pdb=" O PHE A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 209 removed outlier: 3.532A pdb=" N VAL A 209 " --> pdb=" O CYS A 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 206 through 209' Processing helix chain 'E' and resid 29 through 33 removed outlier: 3.702A pdb=" N LYS E 32 " --> pdb=" O ALA E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 208 removed outlier: 3.677A pdb=" N PHE E 206 " --> pdb=" O SER E 203 " (cutoff:3.500A) Proline residue: E 207 - end of helix No H-bonds generated for 'chain 'E' and resid 203 through 208' Processing helix chain 'E' and resid 231 through 233 No H-bonds generated for 'chain 'E' and resid 231 through 233' Processing helix chain 'E' and resid 327 through 333 removed outlier: 3.993A pdb=" N ARG E 331 " --> pdb=" O ALA E 327 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN E 332 " --> pdb=" O GLN E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 375 Processing helix chain 'E' and resid 387 through 390 No H-bonds generated for 'chain 'E' and resid 387 through 390' Processing helix chain 'E' and resid 395 through 398 No H-bonds generated for 'chain 'E' and resid 395 through 398' Processing helix chain 'E' and resid 526 through 531 Processing helix chain 'E' and resid 614 through 616 No H-bonds generated for 'chain 'E' and resid 614 through 616' Processing helix chain 'D' and resid 67 through 75 Processing helix chain 'D' and resid 122 through 126 Processing helix chain 'D' and resid 163 through 166 No H-bonds generated for 'chain 'D' and resid 163 through 166' Processing helix chain 'D' and resid 206 through 209 No H-bonds generated for 'chain 'D' and resid 206 through 209' Processing helix chain 'D' and resid 339 through 346 removed outlier: 3.920A pdb=" N LYS D 345 " --> pdb=" O PRO D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 425 Processing helix chain 'D' and resid 533 through 535 No H-bonds generated for 'chain 'D' and resid 533 through 535' Processing helix chain 'D' and resid 639 through 646 Processing helix chain 'D' and resid 709 through 720 removed outlier: 5.468A pdb=" N LYS D 714 " --> pdb=" O TYR D 711 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 42 through 46 removed outlier: 3.735A pdb=" N SER A 45 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 49 through 51 Processing sheet with id= C, first strand: chain 'A' and resid 60 through 62 removed outlier: 4.032A pdb=" N LYS A 60 " --> pdb=" O TRP A 98 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLN A 95 " --> pdb=" O ASP A 90 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASP A 90 " --> pdb=" O GLN A 95 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 188 through 190 Processing sheet with id= E, first strand: chain 'A' and resid 270 through 272 Processing sheet with id= F, first strand: chain 'E' and resid 45 through 47 Processing sheet with id= G, first strand: chain 'E' and resid 52 through 58 removed outlier: 6.858A pdb=" N GLY E 65 " --> pdb=" O GLN E 53 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N VAL E 55 " --> pdb=" O PHE E 63 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N PHE E 63 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU E 57 " --> pdb=" O HIS E 61 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N HIS E 61 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA E 82 " --> pdb=" O VAL E 72 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 89 through 91 removed outlier: 3.735A pdb=" N LYS E 113 " --> pdb=" O VAL E 89 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 119 through 123 removed outlier: 3.629A pdb=" N ALA E 119 " --> pdb=" O CYS E 133 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N GLU E 157 " --> pdb=" O VAL E 145 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 182 through 188 Processing sheet with id= K, first strand: chain 'E' and resid 417 through 419 removed outlier: 7.036A pdb=" N TYR E 291 " --> pdb=" O THR E 418 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL E 264 " --> pdb=" O TYR E 249 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N TYR E 249 " --> pdb=" O VAL E 264 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 424 through 427 removed outlier: 4.002A pdb=" N CYS E 298 " --> pdb=" O PHE E 314 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 320 through 324 Processing sheet with id= N, first strand: chain 'E' and resid 444 through 447 Processing sheet with id= O, first strand: chain 'E' and resid 461 through 464 removed outlier: 4.315A pdb=" N PHE E 479 " --> pdb=" O PHE E 462 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL E 477 " --> pdb=" O GLN E 464 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 538 through 540 Processing sheet with id= Q, first strand: chain 'E' and resid 621 through 625 removed outlier: 6.635A pdb=" N TRP E 586 " --> pdb=" O ILE E 565 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ILE E 565 " --> pdb=" O TRP E 586 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 601 through 605 Processing sheet with id= S, first strand: chain 'E' and resid 707 through 710 removed outlier: 3.908A pdb=" N SER E 661 " --> pdb=" O THR E 678 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ASN E 680 " --> pdb=" O ILE E 659 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N ILE E 659 " --> pdb=" O ASN E 680 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 719 through 721 removed outlier: 3.957A pdb=" N PHE E 720 " --> pdb=" O PHE E 736 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE E 736 " --> pdb=" O PHE E 720 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'E' and resid 347 through 349 removed outlier: 4.642A pdb=" N ARG E 359 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 49 through 52 Processing sheet with id= W, first strand: chain 'D' and resid 95 through 99 removed outlier: 3.938A pdb=" N GLN D 95 " --> pdb=" O ASP D 90 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ASP D 90 " --> pdb=" O GLN D 95 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 270 through 272 Processing sheet with id= Y, first strand: chain 'D' and resid 563 through 565 removed outlier: 3.880A pdb=" N CYS D 519 " --> pdb=" O LEU D 511 " (cutoff:3.500A) removed outlier: 8.837A pdb=" N GLY D 520 " --> pdb=" O ALA D 532 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ALA D 532 " --> pdb=" O GLY D 520 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TRP D 528 " --> pdb=" O ILE D 524 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 614 through 616 Processing sheet with id= AA, first strand: chain 'D' and resid 656 through 659 removed outlier: 3.593A pdb=" N VAL D 707 " --> pdb=" O VAL D 690 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU D 677 " --> pdb=" O LEU D 688 " (cutoff:3.500A) 219 hydrogen bonds defined for protein. 558 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: 3.75 Time building geometry restraints manager: 6.15 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: 2206 1.32 - 1.45: 3523 1.45 - 1.58: 6950 1.58 - 1.71: 6 1.71 - 1.83: 139 Bond restraints: 12824 Sorted by residual: bond pdb=" O6 SGN F 3 " pdb=" S2 SGN F 3 " ideal model delta sigma weight residual 1.660 1.526 0.134 2.00e-02 2.50e+03 4.52e+01 bond pdb=" O6 SGN J 3 " pdb=" S2 SGN J 3 " ideal model delta sigma weight residual 1.660 1.526 0.134 2.00e-02 2.50e+03 4.51e+01 bond pdb=" O6 SGN J 1 " pdb=" S2 SGN J 1 " ideal model delta sigma weight residual 1.660 1.528 0.132 2.00e-02 2.50e+03 4.35e+01 bond pdb=" O6 SGN F 1 " pdb=" S2 SGN F 1 " ideal model delta sigma weight residual 1.660 1.529 0.131 2.00e-02 2.50e+03 4.30e+01 bond pdb=" O2 IDS F 6 " pdb=" S IDS F 6 " ideal model delta sigma weight residual 1.646 1.528 0.118 2.00e-02 2.50e+03 3.51e+01 ... (remaining 12819 not shown) Histogram of bond angle deviations from ideal: 98.18 - 105.43: 339 105.43 - 112.69: 6579 112.69 - 119.94: 4817 119.94 - 127.20: 5517 127.20 - 134.46: 174 Bond angle restraints: 17426 Sorted by residual: angle pdb=" N PRO E 88 " pdb=" CA PRO E 88 " pdb=" C PRO E 88 " ideal model delta sigma weight residual 111.21 101.94 9.27 1.59e+00 3.96e-01 3.40e+01 angle pdb=" N ASN D 352 " pdb=" CA ASN D 352 " pdb=" C ASN D 352 " ideal model delta sigma weight residual 113.01 106.61 6.40 1.20e+00 6.94e-01 2.84e+01 angle pdb=" CA ASN D 179 " pdb=" C ASN D 179 " pdb=" N PRO D 180 " ideal model delta sigma weight residual 119.12 124.71 -5.59 1.05e+00 9.07e-01 2.84e+01 angle pdb=" N THR D 368 " pdb=" CA THR D 368 " pdb=" C THR D 368 " ideal model delta sigma weight residual 111.71 105.67 6.04 1.15e+00 7.56e-01 2.76e+01 angle pdb=" N ILE D 39 " pdb=" CA ILE D 39 " pdb=" C ILE D 39 " ideal model delta sigma weight residual 110.62 105.47 5.15 1.02e+00 9.61e-01 2.55e+01 ... (remaining 17421 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 6469 17.97 - 35.93: 818 35.93 - 53.90: 274 53.90 - 71.87: 72 71.87 - 89.83: 19 Dihedral angle restraints: 7652 sinusoidal: 3081 harmonic: 4571 Sorted by residual: dihedral pdb=" CB CYS E 541 " pdb=" SG CYS E 541 " pdb=" SG CYS E 551 " pdb=" CB CYS E 551 " ideal model delta sinusoidal sigma weight residual 93.00 -178.07 -88.93 1 1.00e+01 1.00e-02 9.42e+01 dihedral pdb=" CB CYS D 612 " pdb=" SG CYS D 612 " pdb=" SG CYS D 679 " pdb=" CB CYS D 679 " ideal model delta sinusoidal sigma weight residual -86.00 1.01 -87.01 1 1.00e+01 1.00e-02 9.10e+01 dihedral pdb=" CB CYS A 177 " pdb=" SG CYS A 177 " pdb=" SG CYS A 201 " pdb=" CB CYS A 201 " ideal model delta sinusoidal sigma weight residual -86.00 -172.13 86.13 1 1.00e+01 1.00e-02 8.95e+01 ... (remaining 7649 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1250 0.064 - 0.128: 465 0.128 - 0.193: 144 0.193 - 0.257: 36 0.257 - 0.321: 9 Chirality restraints: 1904 Sorted by residual: chirality pdb=" C1 IDS F 4 " pdb=" O4 SGN F 3 " pdb=" C2 IDS F 4 " pdb=" O5 IDS F 4 " both_signs ideal model delta sigma weight residual False -2.40 -2.30 -0.10 2.00e-02 2.50e+03 2.71e+01 chirality pdb=" C1 SGN F 5 " pdb=" O4 IDS F 4 " pdb=" C2 SGN F 5 " pdb=" O5 SGN F 5 " both_signs ideal model delta sigma weight residual False 2.40 2.31 0.09 2.00e-02 2.50e+03 2.00e+01 chirality pdb=" C1 IDS J 4 " pdb=" O4 SGN J 3 " pdb=" C2 IDS J 4 " pdb=" O5 IDS J 4 " both_signs ideal model delta sigma weight residual False -2.40 -2.47 0.07 2.00e-02 2.50e+03 1.33e+01 ... (remaining 1901 not shown) Planarity restraints: 2235 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 192 " 0.031 2.00e-02 2.50e+03 2.62e-02 1.20e+01 pdb=" CG PHE E 192 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 PHE E 192 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE E 192 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE E 192 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE E 192 " 0.014 2.00e-02 2.50e+03 pdb=" CZ PHE E 192 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 253 " 0.014 2.00e-02 2.50e+03 2.95e-02 8.70e+00 pdb=" C LYS A 253 " -0.051 2.00e-02 2.50e+03 pdb=" O LYS A 253 " 0.019 2.00e-02 2.50e+03 pdb=" N GLY A 254 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 426 " -0.077 9.50e-02 1.11e+02 4.24e-02 8.43e+00 pdb=" NE ARG E 426 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG E 426 " -0.047 2.00e-02 2.50e+03 pdb=" NH1 ARG E 426 " 0.017 2.00e-02 2.50e+03 pdb=" NH2 ARG E 426 " 0.013 2.00e-02 2.50e+03 ... (remaining 2232 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 204 2.57 - 3.15: 11094 3.15 - 3.73: 20080 3.73 - 4.32: 28001 4.32 - 4.90: 43513 Nonbonded interactions: 102892 Sorted by model distance: nonbonded pdb=" OG1 THR E 222 " pdb=" OD1 ASP E 224 " model vdw 1.983 2.440 nonbonded pdb=" O ARG D 126 " pdb=" OD1 ASN D 127 " model vdw 2.042 3.040 nonbonded pdb=" OD1 ASP A 275 " pdb=" ND1 HIS A 277 " model vdw 2.103 2.520 nonbonded pdb=" O SER D 538 " pdb=" OH TYR D 544 " model vdw 2.105 2.440 nonbonded pdb=" OG1 THR D 454 " pdb=" O ILE D 459 " model vdw 2.110 2.440 ... (remaining 102887 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 'F' 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 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: 1.000 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: 5.310 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 36.220 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 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 : 0.011 0.134 12824 Z= 0.724 Angle : 1.368 12.740 17426 Z= 0.840 Chirality : 0.077 0.321 1904 Planarity : 0.006 0.069 2235 Dihedral : 18.233 89.834 4590 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 27.58 Ramachandran Plot: Outliers : 0.45 % Allowed : 8.56 % Favored : 90.99 % Rotamer Outliers : 10.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.78 % 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: -1.69 (0.21), residues: 1554 helix: -0.42 (0.51), residues: 118 sheet: -1.12 (0.27), residues: 338 loop : -1.25 (0.18), residues: 1098 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 146 time to evaluate : 1.478 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 138 outliers final: 28 residues processed: 270 average time/residue: 0.3052 time to fit residues: 110.4983 Evaluate side-chains 103 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 75 time to evaluate : 1.666 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 28 outliers final: 1 residues processed: 28 average time/residue: 0.2428 time to fit residues: 11.8186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 122 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 141 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 HIS ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 GLN E 159 HIS ** E 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 558 GLN ** E 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 343 ASN D 352 ASN D 371 ASN ** D 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 681 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.068 12824 Z= 0.353 Angle : 0.828 12.913 17426 Z= 0.421 Chirality : 0.050 0.245 1904 Planarity : 0.006 0.080 2235 Dihedral : 6.787 58.544 1720 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 29.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.66 % Favored : 94.27 % Rotamer Outliers : 0.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.78 % 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: -1.53 (0.21), residues: 1554 helix: -0.73 (0.50), residues: 113 sheet: -0.74 (0.27), residues: 345 loop : -1.18 (0.18), residues: 1096 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 78 time to evaluate : 1.580 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 outliers start: 10 outliers final: 8 residues processed: 88 average time/residue: 0.2631 time to fit residues: 34.5111 Evaluate side-chains 69 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 61 time to evaluate : 1.701 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1179 time to fit residues: 4.1332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 117 optimal weight: 10.0000 chunk 96 optimal weight: 0.9980 chunk 39 optimal weight: 7.9990 chunk 141 optimal weight: 8.9990 chunk 153 optimal weight: 10.0000 chunk 126 optimal weight: 0.7980 chunk 140 optimal weight: 7.9990 chunk 48 optimal weight: 0.8980 chunk 113 optimal weight: 5.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 95 GLN A 160 HIS ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 HIS ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 199 ASN E 620 ASN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 425 HIS D 534 GLN ** D 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 12824 Z= 0.216 Angle : 0.717 16.494 17426 Z= 0.355 Chirality : 0.048 0.244 1904 Planarity : 0.005 0.047 2235 Dihedral : 6.353 57.371 1720 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 21.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.34 % Favored : 94.59 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.21), residues: 1554 helix: -0.73 (0.50), residues: 112 sheet: -0.69 (0.28), residues: 335 loop : -0.95 (0.19), residues: 1107 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 90 time to evaluate : 1.725 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 outliers start: 4 outliers final: 0 residues processed: 94 average time/residue: 0.2763 time to fit residues: 38.0040 Evaluate side-chains 67 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 1.609 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 9.9990 chunk 106 optimal weight: 50.0000 chunk 73 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 95 optimal weight: 30.0000 chunk 142 optimal weight: 9.9990 chunk 150 optimal weight: 30.0000 chunk 74 optimal weight: 0.0000 chunk 134 optimal weight: 0.9990 chunk 40 optimal weight: 0.4980 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 HIS ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 405 ASN E 528 GLN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 12824 Z= 0.180 Angle : 0.677 14.043 17426 Z= 0.332 Chirality : 0.046 0.206 1904 Planarity : 0.004 0.048 2235 Dihedral : 5.921 57.444 1720 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 18.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.34 % Favored : 94.59 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.78 % 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: -1.17 (0.21), residues: 1554 helix: -0.95 (0.48), residues: 123 sheet: -0.51 (0.28), residues: 336 loop : -0.86 (0.19), residues: 1095 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 87 time to evaluate : 1.694 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 outliers start: 1 outliers final: 0 residues processed: 88 average time/residue: 0.2941 time to fit residues: 40.0669 Evaluate side-chains 65 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 1.593 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 7.9990 chunk 85 optimal weight: 8.9990 chunk 2 optimal weight: 9.9990 chunk 112 optimal weight: 30.0000 chunk 62 optimal weight: 5.9990 chunk 128 optimal weight: 6.9990 chunk 104 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 76 optimal weight: 7.9990 chunk 135 optimal weight: 1.9990 chunk 38 optimal weight: 9.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 GLN ** E 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 516 ASN E 680 ASN D 95 GLN ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 277 HIS ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.4931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.067 12824 Z= 0.401 Angle : 0.781 13.638 17426 Z= 0.394 Chirality : 0.046 0.185 1904 Planarity : 0.006 0.054 2235 Dihedral : 6.296 58.994 1720 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 31.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.86 % Favored : 94.08 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.78 % 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: -1.45 (0.21), residues: 1554 helix: -1.13 (0.47), residues: 119 sheet: -0.54 (0.28), residues: 338 loop : -1.12 (0.18), residues: 1097 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 1.582 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: 0 outliers final: 0 residues processed: 67 average time/residue: 0.2772 time to fit residues: 27.8354 Evaluate side-chains 57 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 1.601 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 3.9990 chunk 135 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 88 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 150 optimal weight: 9.9990 chunk 125 optimal weight: 9.9990 chunk 69 optimal weight: 6.9990 chunk 12 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 528 GLN E 704 ASN D 95 GLN ** D 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.5114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 12824 Z= 0.194 Angle : 0.660 12.329 17426 Z= 0.328 Chirality : 0.046 0.186 1904 Planarity : 0.005 0.049 2235 Dihedral : 5.917 59.232 1720 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 20.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.15 % Favored : 94.79 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.78 % 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: -1.28 (0.21), residues: 1554 helix: -1.20 (0.47), residues: 119 sheet: -0.43 (0.28), residues: 343 loop : -0.98 (0.19), residues: 1092 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 1.511 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: 74 average time/residue: 0.2471 time to fit residues: 27.6943 Evaluate side-chains 62 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 1.453 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 0.9990 chunk 17 optimal weight: 9.9990 chunk 85 optimal weight: 5.9990 chunk 110 optimal weight: 0.0050 chunk 127 optimal weight: 20.0000 chunk 84 optimal weight: 0.9980 chunk 150 optimal weight: 20.0000 chunk 94 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 69 optimal weight: 7.9990 chunk 93 optimal weight: 9.9990 overall best weight: 2.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.5360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 12824 Z= 0.208 Angle : 0.638 10.495 17426 Z= 0.317 Chirality : 0.045 0.227 1904 Planarity : 0.004 0.049 2235 Dihedral : 5.774 59.424 1720 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 21.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.73 % Favored : 94.21 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.78 % 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: -1.23 (0.21), residues: 1554 helix: -1.03 (0.48), residues: 118 sheet: -0.50 (0.28), residues: 345 loop : -0.92 (0.19), residues: 1091 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 1.704 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: 69 average time/residue: 0.2767 time to fit residues: 28.8550 Evaluate side-chains 58 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 1.577 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 20.0000 chunk 89 optimal weight: 0.9980 chunk 45 optimal weight: 9.9990 chunk 29 optimal weight: 4.9990 chunk 95 optimal weight: 7.9990 chunk 102 optimal weight: 9.9990 chunk 74 optimal weight: 0.2980 chunk 14 optimal weight: 8.9990 chunk 118 optimal weight: 0.9990 chunk 136 optimal weight: 8.9990 chunk 144 optimal weight: 8.9990 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 233 GLN D 327 GLN ** D 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.5664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 12824 Z= 0.228 Angle : 0.644 10.309 17426 Z= 0.319 Chirality : 0.045 0.202 1904 Planarity : 0.004 0.050 2235 Dihedral : 5.747 59.093 1720 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 23.33 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.73 % Favored : 94.21 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.78 % 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: -1.25 (0.21), residues: 1554 helix: -1.00 (0.48), residues: 118 sheet: -0.56 (0.28), residues: 347 loop : -0.92 (0.19), residues: 1089 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.668 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: 66 average time/residue: 0.2542 time to fit residues: 26.3980 Evaluate side-chains 57 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 1.646 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 10.0000 chunk 140 optimal weight: 9.9990 chunk 144 optimal weight: 20.0000 chunk 84 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 126 optimal weight: 10.0000 chunk 132 optimal weight: 1.9990 chunk 139 optimal weight: 5.9990 chunk 92 optimal weight: 0.1980 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.5930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 12824 Z= 0.228 Angle : 0.646 10.839 17426 Z= 0.323 Chirality : 0.045 0.202 1904 Planarity : 0.005 0.051 2235 Dihedral : 5.764 59.080 1720 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 23.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.05 % Favored : 93.89 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.78 % 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: -1.18 (0.21), residues: 1554 helix: -0.77 (0.50), residues: 112 sheet: -0.50 (0.29), residues: 328 loop : -0.90 (0.19), residues: 1114 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 66 time to evaluate : 1.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 66 average time/residue: 0.2741 time to fit residues: 27.6946 Evaluate side-chains 56 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 1.561 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 0.9990 chunk 90 optimal weight: 9.9990 chunk 70 optimal weight: 8.9990 chunk 102 optimal weight: 0.7980 chunk 155 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 123 optimal weight: 20.0000 chunk 12 optimal weight: 9.9990 chunk 95 optimal weight: 20.0000 chunk 75 optimal weight: 5.9990 chunk 98 optimal weight: 9.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 117 ASN D 551 HIS ** D 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.6056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 12824 Z= 0.198 Angle : 0.634 9.147 17426 Z= 0.316 Chirality : 0.045 0.178 1904 Planarity : 0.004 0.051 2235 Dihedral : 5.651 58.946 1720 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 20.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.53 % Favored : 94.40 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.78 % 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: -1.17 (0.21), residues: 1554 helix: -0.65 (0.50), residues: 112 sheet: -0.55 (0.28), residues: 340 loop : -0.89 (0.19), residues: 1102 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 66 time to evaluate : 1.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 66 average time/residue: 0.2405 time to fit residues: 25.3611 Evaluate side-chains 54 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 1.572 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 7.9990 chunk 37 optimal weight: 0.3980 chunk 114 optimal weight: 0.0470 chunk 18 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 123 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 127 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 108 optimal weight: 0.0020 overall best weight: 0.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 717 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.039066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.030413 restraints weight = 169080.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.031152 restraints weight = 113080.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.031691 restraints weight = 83004.741| |-----------------------------------------------------------------------------| r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.6149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 12824 Z= 0.164 Angle : 0.632 9.008 17426 Z= 0.311 Chirality : 0.046 0.250 1904 Planarity : 0.004 0.052 2235 Dihedral : 5.318 58.857 1720 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.76 % Favored : 95.17 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.21), residues: 1554 helix: -0.60 (0.50), residues: 115 sheet: -0.39 (0.28), residues: 336 loop : -0.89 (0.19), residues: 1103 =============================================================================== Job complete usr+sys time: 2109.76 seconds wall clock time: 39 minutes 51.70 seconds (2391.70 seconds total)