Starting phenix.real_space_refine (version: dev) on Mon Dec 12 22:42:27 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7moa_23922/12_2022/7moa_23922_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7moa_23922/12_2022/7moa_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_23922/12_2022/7moa_23922.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7moa_23922/12_2022/7moa_23922.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7moa_23922/12_2022/7moa_23922_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7moa_23922/12_2022/7moa_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 Convert atoms to be neutral 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-dev-4807/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: 7.11, per 1000 atoms: 0.57 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: 5.36 Conformation dependent library (CDL) restraints added in 1.8 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: 1.46 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: 3.53 Time building geometry restraints manager: 5.74 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 1.651 1.528 0.123 2.00e-02 2.50e+03 3.81e+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: 6468 17.97 - 35.93: 817 35.93 - 53.90: 277 53.90 - 71.87: 71 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: 1259 0.064 - 0.128: 463 0.128 - 0.193: 138 0.193 - 0.257: 35 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 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. 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: 1.440 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: 5.430 Check model and map are aligned: 0.170 Convert atoms to be neutral: 0.090 Process input model: 33.730 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 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= 0.715 Angle : 1.356 12.740 17426 Z= 0.838 Chirality : 0.076 0.321 1904 Planarity : 0.006 0.069 2235 Dihedral : 18.238 89.834 4590 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 27.95 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 : 1.615 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: 0.2992 time to fit residues: 109.8940 Evaluate side-chains 103 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 75 time to evaluate : 1.633 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 28 outliers final: 1 residues processed: 28 average time/residue: 0.2379 time to fit residues: 11.5179 ------------------------------------------------------------------------------- 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 D 681 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.081 12824 Z= 0.361 Angle : 0.819 12.901 17426 Z= 0.416 Chirality : 0.050 0.229 1904 Planarity : 0.006 0.077 2235 Dihedral : 6.826 57.564 1720 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 30.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.92 % Favored : 94.02 % Rotamer Outliers : 0.67 % 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: -1.52 (0.21), residues: 1554 helix: -0.63 (0.51), residues: 113 sheet: -0.76 (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 89 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 80 time to evaluate : 1.483 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: 9 outliers final: 7 residues processed: 89 average time/residue: 0.2386 time to fit residues: 32.0222 Evaluate side-chains 68 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 61 time to evaluate : 1.494 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1085 time to fit residues: 3.3972 ------------------------------------------------------------------------------- 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: 30.0000 chunk 43 optimal weight: 5.9990 chunk 117 optimal weight: 10.0000 chunk 96 optimal weight: 0.6980 chunk 39 optimal weight: 9.9990 chunk 141 optimal weight: 6.9990 chunk 153 optimal weight: 10.0000 chunk 126 optimal weight: 4.9990 chunk 140 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 113 optimal weight: 4.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 HIS ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 GLN E 58 HIS ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 528 GLN E 620 ASN E 680 ASN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN ** D 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 425 HIS ** D 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 12824 Z= 0.260 Angle : 0.723 16.743 17426 Z= 0.362 Chirality : 0.047 0.263 1904 Planarity : 0.005 0.058 2235 Dihedral : 6.431 57.938 1720 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 25.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.60 % Favored : 94.34 % 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: -1.33 (0.21), residues: 1554 helix: -0.71 (0.50), residues: 112 sheet: -0.78 (0.27), residues: 343 loop : -0.96 (0.19), residues: 1099 *********************** 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 85 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 81 time to evaluate : 1.771 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 outliers start: 4 outliers final: 1 residues processed: 85 average time/residue: 0.2748 time to fit residues: 34.2124 Evaluate side-chains 67 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 66 time to evaluate : 1.561 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1108 time to fit residues: 2.3851 ------------------------------------------------------------------------------- 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: 20.0000 chunk 106 optimal weight: 50.0000 chunk 73 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 67 optimal weight: 6.9990 chunk 95 optimal weight: 30.0000 chunk 142 optimal weight: 9.9990 chunk 150 optimal weight: 20.0000 chunk 74 optimal weight: 3.9990 chunk 134 optimal weight: 7.9990 chunk 40 optimal weight: 8.9990 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 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 199 ASN ** E 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 332 GLN ** E 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 516 ASN E 528 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: 0.7875 moved from start: 0.4945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.075 12824 Z= 0.403 Angle : 0.798 14.365 17426 Z= 0.406 Chirality : 0.048 0.227 1904 Planarity : 0.006 0.062 2235 Dihedral : 6.697 52.888 1720 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 33.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.56 % Favored : 93.37 % 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: -1.53 (0.21), residues: 1554 helix: -1.14 (0.48), residues: 119 sheet: -0.61 (0.28), residues: 328 loop : -1.17 (0.18), residues: 1107 *********************** 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 71 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 70 time to evaluate : 1.706 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: 71 average time/residue: 0.2727 time to fit residues: 29.8645 Evaluate side-chains 58 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 1.452 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1173 ------------------------------------------------------------------------------- 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: 1.9990 chunk 85 optimal weight: 9.9990 chunk 2 optimal weight: 20.0000 chunk 112 optimal weight: 10.0000 chunk 62 optimal weight: 8.9990 chunk 128 optimal weight: 20.0000 chunk 104 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 76 optimal weight: 10.0000 chunk 135 optimal weight: 7.9990 chunk 38 optimal weight: 9.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- 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 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 332 GLN ** E 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 542 HIS E 704 ASN ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 327 GLN ** D 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.5985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.074 12824 Z= 0.458 Angle : 0.864 19.534 17426 Z= 0.441 Chirality : 0.049 0.254 1904 Planarity : 0.007 0.079 2235 Dihedral : 7.096 46.897 1720 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 39.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.79 % Favored : 92.15 % 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: -1.90 (0.20), residues: 1554 helix: -1.73 (0.43), residues: 119 sheet: -1.01 (0.27), residues: 333 loop : -1.35 (0.18), residues: 1102 *********************** 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 64 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 1.382 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: 64 average time/residue: 0.2615 time to fit residues: 25.6194 Evaluate side-chains 53 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 1.491 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0314 ------------------------------------------------------------------------------- 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: 2.9990 chunk 135 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 150 optimal weight: 10.0000 chunk 125 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 79 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.6205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 12824 Z= 0.300 Angle : 0.719 11.907 17426 Z= 0.364 Chirality : 0.047 0.217 1904 Planarity : 0.005 0.045 2235 Dihedral : 6.686 47.953 1720 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 30.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.27 % Favored : 92.66 % 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: -1.77 (0.20), residues: 1554 helix: -1.70 (0.44), residues: 119 sheet: -0.84 (0.27), residues: 332 loop : -1.28 (0.18), residues: 1103 *********************** 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 63 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 1.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.2305 time to fit residues: 23.4681 Evaluate side-chains 52 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 1.567 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0629 ------------------------------------------------------------------------------- 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: 8.9990 chunk 17 optimal weight: 2.9990 chunk 85 optimal weight: 7.9990 chunk 110 optimal weight: 0.6980 chunk 127 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 150 optimal weight: 30.0000 chunk 94 optimal weight: 3.9990 chunk 91 optimal weight: 0.4980 chunk 69 optimal weight: 0.7980 chunk 93 optimal weight: 20.0000 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN 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 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 233 GLN ** D 497 ASN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.6232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 12824 Z= 0.199 Angle : 0.660 11.374 17426 Z= 0.328 Chirality : 0.046 0.235 1904 Planarity : 0.005 0.048 2235 Dihedral : 6.211 48.856 1720 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 22.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.24 % Favored : 93.69 % 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: -1.50 (0.21), residues: 1554 helix: -1.49 (0.43), residues: 128 sheet: -0.76 (0.27), residues: 326 loop : -1.03 (0.19), residues: 1100 *********************** 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 63 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 1.628 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: 63 average time/residue: 0.2278 time to fit residues: 23.3744 Evaluate side-chains 56 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 1.594 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1781 ------------------------------------------------------------------------------- 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: 0.2980 chunk 45 optimal weight: 0.9980 chunk 29 optimal weight: 10.0000 chunk 95 optimal weight: 30.0000 chunk 102 optimal weight: 50.0000 chunk 74 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 136 optimal weight: 6.9990 chunk 144 optimal weight: 5.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- 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 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 497 ASN ** 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: 0.7895 moved from start: 0.6386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 12824 Z= 0.217 Angle : 0.651 10.784 17426 Z= 0.325 Chirality : 0.046 0.242 1904 Planarity : 0.004 0.047 2235 Dihedral : 6.063 48.852 1720 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 23.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.79 % Favored : 94.14 % 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: -1.41 (0.21), residues: 1554 helix: -1.42 (0.44), residues: 128 sheet: -0.73 (0.28), residues: 328 loop : -0.96 (0.19), residues: 1098 *********************** 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 61 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 60 time to evaluate : 1.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 60 average time/residue: 0.2303 time to fit residues: 22.2158 Evaluate side-chains 52 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 1.404 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9103 ------------------------------------------------------------------------------- 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: 6.9990 chunk 140 optimal weight: 7.9990 chunk 144 optimal weight: 6.9990 chunk 84 optimal weight: 20.0000 chunk 61 optimal weight: 20.0000 chunk 110 optimal weight: 7.9990 chunk 42 optimal weight: 0.0870 chunk 126 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 139 optimal weight: 10.0000 chunk 92 optimal weight: 9.9990 overall best weight: 4.2166 ------------------------------------------------------------------------------- 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 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 497 ASN ** 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: 0.7932 moved from start: 0.6724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 12824 Z= 0.287 Angle : 0.684 11.227 17426 Z= 0.346 Chirality : 0.046 0.235 1904 Planarity : 0.005 0.060 2235 Dihedral : 6.230 50.096 1720 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 28.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.46 % Favored : 92.47 % 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: -1.46 (0.21), residues: 1554 helix: -1.13 (0.46), residues: 116 sheet: -0.94 (0.28), residues: 319 loop : -0.98 (0.19), residues: 1119 *********************** 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 57 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 56 time to evaluate : 1.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 56 average time/residue: 0.2385 time to fit residues: 21.7538 Evaluate side-chains 52 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 1.589 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1350 ------------------------------------------------------------------------------- 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: 0.7980 chunk 90 optimal weight: 0.8980 chunk 70 optimal weight: 6.9990 chunk 102 optimal weight: 10.0000 chunk 155 optimal weight: 0.8980 chunk 143 optimal weight: 9.9990 chunk 123 optimal weight: 20.0000 chunk 12 optimal weight: 9.9990 chunk 95 optimal weight: 20.0000 chunk 75 optimal weight: 9.9990 chunk 98 optimal weight: 6.9990 overall best weight: 3.3184 ------------------------------------------------------------------------------- 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 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 497 ASN ** 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: 0.7916 moved from start: 0.6859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 12824 Z= 0.233 Angle : 0.655 10.047 17426 Z= 0.330 Chirality : 0.046 0.225 1904 Planarity : 0.005 0.045 2235 Dihedral : 6.145 51.216 1720 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 24.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.69 % Favored : 93.24 % 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: -1.41 (0.21), residues: 1554 helix: -1.14 (0.46), residues: 116 sheet: -0.90 (0.28), residues: 326 loop : -0.95 (0.19), residues: 1112 ********************** 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 57 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 56 time to evaluate : 1.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 56 average time/residue: 0.2349 time to fit residues: 21.3225 Evaluate side-chains 50 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 1.511 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9660 ------------------------------------------------------------------------------- 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: 5.9990 chunk 37 optimal weight: 4.9990 chunk 114 optimal weight: 7.9990 chunk 18 optimal weight: 20.0000 chunk 34 optimal weight: 0.9980 chunk 123 optimal weight: 9.9990 chunk 51 optimal weight: 0.8980 chunk 127 optimal weight: 20.0000 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 108 optimal weight: 10.0000 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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 ** E 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.037343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.028840 restraints weight = 176763.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.029571 restraints weight = 118417.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.030068 restraints weight = 86765.286| |-----------------------------------------------------------------------------| r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.7000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 12824 Z= 0.211 Angle : 0.630 8.677 17426 Z= 0.316 Chirality : 0.045 0.211 1904 Planarity : 0.005 0.043 2235 Dihedral : 5.955 52.077 1720 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 22.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.95 % Favored : 92.99 % 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: -1.35 (0.21), residues: 1554 helix: -0.96 (0.47), residues: 116 sheet: -0.87 (0.28), residues: 326 loop : -0.91 (0.19), residues: 1112 =============================================================================== Job complete usr+sys time: 2001.81 seconds wall clock time: 38 minutes 21.17 seconds (2301.17 seconds total)