Starting phenix.real_space_refine on Fri Mar 15 19:04:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7moa_23922/03_2024/7moa_23922_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7moa_23922/03_2024/7moa_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_23922/03_2024/7moa_23922.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7moa_23922/03_2024/7moa_23922.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7moa_23922/03_2024/7moa_23922_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7moa_23922/03_2024/7moa_23922_updated.pdb" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 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-dev-5265/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: 28 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: 28 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 7.05, per 1000 atoms: 0.56 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: 5.45 Conformation dependent library (CDL) restraints added in 2.3 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: 2.85 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: 4.11 Time building geometry restraints manager: 5.89 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 - 25.85: 7052 25.85 - 51.71: 645 51.71 - 77.56: 129 77.56 - 103.41: 36 103.41 - 129.26: 36 Dihedral angle restraints: 7898 sinusoidal: 3327 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 7895 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: 1.040 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: 0.000 Extract box with map and model: 4.780 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 37.180 Find NCS groups from input model: 0.420 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: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.480 ------------------------------------------------------------------------------- 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 : 22.294 129.263 4836 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 % Allowed : 5.64 % Favored : 84.11 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP D 547 HIS 0.009 0.002 HIS D 448 PHE 0.056 0.003 PHE E 192 TYR 0.022 0.003 TYR E 501 ARG 0.048 0.002 ARG E 426 *********************** 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 : 1.526 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 REVERT: A 170 LYS cc_start: 0.7501 (OUTLIER) cc_final: 0.6309 (tptt) REVERT: E 118 MET cc_start: 0.9125 (mtt) cc_final: 0.8578 (pmm) REVERT: E 227 MET cc_start: 0.9205 (ptt) cc_final: 0.8953 (mtm) REVERT: E 260 TYR cc_start: 0.9002 (m-80) cc_final: 0.8717 (m-80) REVERT: E 273 THR cc_start: 0.7735 (OUTLIER) cc_final: 0.6827 (p) REVERT: E 291 TYR cc_start: 0.9226 (t80) cc_final: 0.8879 (t80) REVERT: E 293 GLU cc_start: 0.9289 (mt-10) cc_final: 0.8580 (mt-10) REVERT: E 372 ASP cc_start: 0.9657 (t70) cc_final: 0.9430 (t0) REVERT: E 424 LEU cc_start: 0.9487 (tt) cc_final: 0.9145 (tt) REVERT: E 455 LEU cc_start: 0.9115 (mt) cc_final: 0.8891 (mp) REVERT: E 491 ILE cc_start: 0.8894 (OUTLIER) cc_final: 0.8063 (mt) REVERT: E 527 SER cc_start: 0.9632 (OUTLIER) cc_final: 0.9422 (m) REVERT: E 595 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.7921 (tmmt) REVERT: E 651 THR cc_start: 0.8573 (OUTLIER) cc_final: 0.8270 (p) REVERT: E 674 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7037 (tp) REVERT: D 178 ARG cc_start: 0.6226 (OUTLIER) cc_final: 0.5796 (mmt-90) REVERT: D 339 MET cc_start: 0.8610 (mtp) cc_final: 0.8298 (mpp) REVERT: D 340 THR cc_start: 0.7121 (OUTLIER) cc_final: 0.6679 (p) REVERT: D 348 ASP cc_start: 0.3888 (OUTLIER) cc_final: 0.3282 (m-30) REVERT: D 351 GLU cc_start: 0.7799 (tt0) cc_final: 0.6915 (tt0) REVERT: D 374 VAL cc_start: 0.8592 (OUTLIER) cc_final: 0.7978 (p) REVERT: D 579 LEU cc_start: 0.9465 (tp) cc_final: 0.9248 (mt) REVERT: D 686 MET cc_start: 0.9069 (ptm) cc_final: 0.8524 (ptm) outliers start: 138 outliers final: 28 residues processed: 270 average time/residue: 0.3029 time to fit residues: 109.7853 Evaluate side-chains 119 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 80 time to evaluate : 1.506 ------------------------------------------------------------------------------- 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: 6.9990 chunk 40 optimal weight: 6.9990 chunk 79 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 122 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 91 optimal weight: 9.9990 chunk 141 optimal weight: 5.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- 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 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 Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 12824 Z= 0.314 Angle : 0.819 12.804 17426 Z= 0.412 Chirality : 0.051 0.321 1904 Planarity : 0.006 0.082 2235 Dihedral : 19.686 121.815 1966 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 28.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.53 % Favored : 94.40 % Rotamer: Outliers : 0.22 % Allowed : 10.10 % Favored : 89.68 % 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: -0.99 (0.48), residues: 112 sheet: -0.77 (0.27), residues: 347 loop : -1.14 (0.18), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 98 HIS 0.011 0.002 HIS D 337 PHE 0.033 0.002 PHE E 192 TYR 0.030 0.002 TYR A 272 ARG 0.008 0.001 ARG A 93 *********************** 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 86 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 83 time to evaluate : 1.579 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: E 118 MET cc_start: 0.8913 (mtt) cc_final: 0.8571 (pmm) REVERT: E 227 MET cc_start: 0.8911 (ptt) cc_final: 0.8504 (mtm) REVERT: E 292 MET cc_start: 0.8798 (mpp) cc_final: 0.8459 (mpp) REVERT: E 293 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7337 (mt-10) REVERT: E 429 LEU cc_start: 0.9417 (tp) cc_final: 0.9165 (tp) REVERT: E 463 MET cc_start: 0.9123 (mpp) cc_final: 0.8857 (mpp) REVERT: E 464 GLN cc_start: 0.9462 (mt0) cc_final: 0.9223 (mp10) REVERT: D 223 MET cc_start: 0.7326 (tmm) cc_final: 0.7055 (tmm) REVERT: D 419 MET cc_start: 0.8855 (mtt) cc_final: 0.8417 (mtt) REVERT: D 686 MET cc_start: 0.9315 (ptm) cc_final: 0.8681 (ttp) outliers start: 3 outliers final: 3 residues processed: 86 average time/residue: 0.2705 time to fit residues: 33.8201 Evaluate side-chains 70 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 67 time to evaluate : 1.260 ------------------------------------------------------------------------------- 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: 1.9990 chunk 43 optimal weight: 20.0000 chunk 117 optimal weight: 6.9990 chunk 96 optimal weight: 0.5980 chunk 39 optimal weight: 6.9990 chunk 141 optimal weight: 10.0000 chunk 153 optimal weight: 8.9990 chunk 126 optimal weight: 7.9990 chunk 140 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 113 optimal weight: 10.0000 overall best weight: 3.9188 ------------------------------------------------------------------------------- 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 53 GLN E 58 HIS ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 332 GLN ** E 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN ** D 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 425 HIS ** D 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 681 GLN D 717 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 12824 Z= 0.293 Angle : 0.739 16.214 17426 Z= 0.369 Chirality : 0.048 0.315 1904 Planarity : 0.005 0.056 2235 Dihedral : 17.960 121.984 1966 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 27.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.24 % Favored : 93.69 % Rotamer: Outliers : 0.07 % Allowed : 6.53 % Favored : 93.39 % 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: -1.44 (0.21), residues: 1554 helix: -1.04 (0.48), residues: 111 sheet: -0.69 (0.27), residues: 343 loop : -1.06 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 507 HIS 0.013 0.002 HIS A 160 PHE 0.025 0.002 PHE E 192 TYR 0.021 0.002 TYR A 272 ARG 0.010 0.001 ARG D 373 *********************** 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 80 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 79 time to evaluate : 1.627 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: A 114 HIS cc_start: 0.8454 (p-80) cc_final: 0.8223 (p-80) REVERT: E 118 MET cc_start: 0.8825 (mtt) cc_final: 0.8476 (pmm) REVERT: E 262 LEU cc_start: 0.9475 (mp) cc_final: 0.9202 (mp) REVERT: E 291 TYR cc_start: 0.8825 (t80) cc_final: 0.8538 (t80) REVERT: E 294 MET cc_start: 0.9356 (mmm) cc_final: 0.8767 (mmm) REVERT: E 463 MET cc_start: 0.9151 (mpp) cc_final: 0.8857 (mpp) REVERT: D 223 MET cc_start: 0.7548 (tmm) cc_final: 0.7242 (tmm) REVERT: D 419 MET cc_start: 0.8685 (mtt) cc_final: 0.8176 (mtt) REVERT: D 579 LEU cc_start: 0.9216 (mt) cc_final: 0.8901 (mt) outliers start: 1 outliers final: 0 residues processed: 80 average time/residue: 0.2908 time to fit residues: 33.6532 Evaluate side-chains 61 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 1.572 ------------------------------------------------------------------------------- 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: 8.9990 chunk 106 optimal weight: 40.0000 chunk 73 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 67 optimal weight: 7.9990 chunk 95 optimal weight: 20.0000 chunk 142 optimal weight: 10.0000 chunk 150 optimal weight: 20.0000 chunk 74 optimal weight: 7.9990 chunk 134 optimal weight: 5.9990 chunk 40 optimal weight: 20.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- 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 ** 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** E 516 ASN E 528 GLN ** E 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 680 ASN ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 277 HIS ** D 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 681 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.5322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.128 12824 Z= 0.517 Angle : 0.936 14.537 17426 Z= 0.474 Chirality : 0.053 0.348 1904 Planarity : 0.007 0.066 2235 Dihedral : 16.533 123.375 1966 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 43.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.46 % Favored : 92.47 % Rotamer: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % 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: -1.74 (0.43), residues: 120 sheet: -1.00 (0.27), residues: 334 loop : -1.35 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP D 528 HIS 0.012 0.003 HIS A 160 PHE 0.041 0.004 PHE E 192 TYR 0.031 0.003 TYR D 353 ARG 0.010 0.001 ARG A 93 *********************** 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 63 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 1.542 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: E 118 MET cc_start: 0.9185 (mtt) cc_final: 0.8903 (mtp) REVERT: E 292 MET cc_start: 0.8651 (mpp) cc_final: 0.8139 (mpp) REVERT: E 294 MET cc_start: 0.9354 (mmm) cc_final: 0.8751 (mmm) REVERT: D 212 MET cc_start: 0.7006 (ttt) cc_final: 0.6654 (tpp) REVERT: D 223 MET cc_start: 0.7640 (tmm) cc_final: 0.7435 (tmm) REVERT: D 419 MET cc_start: 0.8674 (mtt) cc_final: 0.8370 (mtt) REVERT: D 579 LEU cc_start: 0.9257 (mt) cc_final: 0.8953 (mt) REVERT: D 686 MET cc_start: 0.9146 (ttp) cc_final: 0.8721 (tpp) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.2473 time to fit residues: 24.1678 Evaluate side-chains 54 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 1.524 ------------------------------------------------------------------------------- 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: 9.9990 chunk 85 optimal weight: 9.9990 chunk 2 optimal weight: 20.0000 chunk 112 optimal weight: 20.0000 chunk 62 optimal weight: 10.0000 chunk 128 optimal weight: 0.9980 chunk 104 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 4.9990 chunk 135 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- 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 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 620 ASN E 704 ASN D 95 GLN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.5651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 12824 Z= 0.322 Angle : 0.756 13.517 17426 Z= 0.377 Chirality : 0.050 0.350 1904 Planarity : 0.005 0.056 2235 Dihedral : 15.684 122.799 1966 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 30.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.37 % Favored : 93.56 % Rotamer: Outliers : 0.15 % Allowed : 3.12 % Favored : 96.73 % 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: -1.83 (0.20), residues: 1554 helix: -1.93 (0.44), residues: 121 sheet: -1.16 (0.26), residues: 348 loop : -1.17 (0.19), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 617 HIS 0.017 0.002 HIS A 160 PHE 0.027 0.002 PHE D 706 TYR 0.025 0.002 TYR E 566 ARG 0.015 0.001 ARG D 586 *********************** 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 72 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 70 time to evaluate : 1.424 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: A 206 CYS cc_start: 0.6938 (p) cc_final: 0.6582 (m) REVERT: E 229 LEU cc_start: 0.9382 (mm) cc_final: 0.8273 (tt) REVERT: E 293 GLU cc_start: 0.8702 (mt-10) cc_final: 0.7762 (mt-10) REVERT: E 294 MET cc_start: 0.9275 (mmm) cc_final: 0.8655 (mmm) REVERT: E 620 ASN cc_start: 0.9159 (OUTLIER) cc_final: 0.8925 (t0) REVERT: D 212 MET cc_start: 0.7191 (ttt) cc_final: 0.6504 (tpp) REVERT: D 223 MET cc_start: 0.7708 (tmm) cc_final: 0.7404 (tmm) REVERT: D 353 TYR cc_start: 0.9057 (m-10) cc_final: 0.8742 (m-80) REVERT: D 419 MET cc_start: 0.8635 (mtt) cc_final: 0.8309 (mtt) REVERT: D 579 LEU cc_start: 0.9369 (mt) cc_final: 0.9062 (mt) REVERT: D 686 MET cc_start: 0.9037 (ttp) cc_final: 0.8576 (tpp) outliers start: 2 outliers final: 0 residues processed: 72 average time/residue: 0.2319 time to fit residues: 26.9291 Evaluate side-chains 57 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 56 time to evaluate : 1.190 ------------------------------------------------------------------------------- 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: 1.9990 chunk 135 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 88 optimal weight: 40.0000 chunk 37 optimal weight: 9.9990 chunk 150 optimal weight: 10.0000 chunk 125 optimal weight: 2.9990 chunk 69 optimal weight: 10.0000 chunk 12 optimal weight: 8.9990 chunk 49 optimal weight: 5.9990 chunk 79 optimal weight: 20.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 79 GLN ** 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 D 95 GLN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.6032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 12824 Z= 0.331 Angle : 0.749 11.850 17426 Z= 0.372 Chirality : 0.050 0.377 1904 Planarity : 0.005 0.055 2235 Dihedral : 14.581 122.837 1966 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 32.33 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.46 % Favored : 92.47 % Rotamer: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % 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: -1.83 (0.20), residues: 1554 helix: -1.89 (0.44), residues: 120 sheet: -1.08 (0.27), residues: 330 loop : -1.22 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 617 HIS 0.017 0.002 HIS A 160 PHE 0.019 0.002 PHE D 706 TYR 0.020 0.002 TYR E 84 ARG 0.008 0.001 ARG E 413 *********************** 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 64 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 1.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 219 LEU cc_start: 0.9118 (tp) cc_final: 0.8674 (tp) REVERT: E 229 LEU cc_start: 0.9395 (mm) cc_final: 0.8183 (tt) REVERT: E 292 MET cc_start: 0.9011 (mtm) cc_final: 0.8810 (mtm) REVERT: E 293 GLU cc_start: 0.8545 (mt-10) cc_final: 0.7830 (mt-10) REVERT: E 294 MET cc_start: 0.9175 (mmm) cc_final: 0.8606 (mmm) REVERT: D 212 MET cc_start: 0.7275 (ttt) cc_final: 0.6571 (tpp) REVERT: D 223 MET cc_start: 0.7714 (tmm) cc_final: 0.7372 (tmm) REVERT: D 419 MET cc_start: 0.8619 (mtt) cc_final: 0.8290 (mtt) REVERT: D 579 LEU cc_start: 0.9346 (mt) cc_final: 0.9039 (mt) REVERT: D 686 MET cc_start: 0.9060 (ttp) cc_final: 0.8601 (tpp) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.2293 time to fit residues: 23.5328 Evaluate side-chains 54 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 1.460 ------------------------------------------------------------------------------- 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: 9.9990 chunk 17 optimal weight: 8.9990 chunk 85 optimal weight: 10.0000 chunk 110 optimal weight: 0.5980 chunk 127 optimal weight: 20.0000 chunk 84 optimal weight: 4.9990 chunk 150 optimal weight: 20.0000 chunk 94 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 93 optimal weight: 20.0000 overall best weight: 3.4586 ------------------------------------------------------------------------------- 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** ** E 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN D 233 GLN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.6212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12824 Z= 0.253 Angle : 0.722 11.353 17426 Z= 0.354 Chirality : 0.050 0.378 1904 Planarity : 0.005 0.046 2235 Dihedral : 13.736 121.903 1966 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 27.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.82 % Favored : 93.11 % Rotamer: Outliers : 0.07 % Allowed : 1.63 % Favored : 98.29 % 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: -1.68 (0.20), residues: 1554 helix: -1.81 (0.44), residues: 120 sheet: -1.03 (0.27), residues: 324 loop : -1.09 (0.18), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 617 HIS 0.017 0.002 HIS A 160 PHE 0.017 0.002 PHE D 706 TYR 0.017 0.002 TYR E 566 ARG 0.006 0.001 ARG A 93 *********************** 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 64 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 63 time to evaluate : 1.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 118 MET cc_start: 0.9288 (mtp) cc_final: 0.9064 (mtp) REVERT: E 229 LEU cc_start: 0.9302 (mm) cc_final: 0.8080 (tt) REVERT: E 293 GLU cc_start: 0.8825 (mt-10) cc_final: 0.7892 (mt-10) REVERT: E 294 MET cc_start: 0.9142 (mmm) cc_final: 0.8667 (mmm) REVERT: E 362 MET cc_start: 0.9053 (ppp) cc_final: 0.8843 (ppp) REVERT: E 636 MET cc_start: 0.8976 (ttt) cc_final: 0.8700 (ttt) REVERT: D 212 MET cc_start: 0.7248 (ttt) cc_final: 0.6563 (tpp) REVERT: D 223 MET cc_start: 0.7639 (tmm) cc_final: 0.7214 (tmm) REVERT: D 419 MET cc_start: 0.8539 (mtt) cc_final: 0.8255 (mtt) REVERT: D 579 LEU cc_start: 0.9382 (mt) cc_final: 0.9064 (mt) REVERT: D 686 MET cc_start: 0.9012 (ttp) cc_final: 0.8625 (tpp) outliers start: 1 outliers final: 0 residues processed: 63 average time/residue: 0.2349 time to fit residues: 23.7575 Evaluate side-chains 56 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 1.653 ------------------------------------------------------------------------------- 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: 0.9990 chunk 89 optimal weight: 0.9980 chunk 45 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 chunk 95 optimal weight: 30.0000 chunk 102 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 118 optimal weight: 20.0000 chunk 136 optimal weight: 8.9990 chunk 144 optimal weight: 8.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- 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 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** ** D 238 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.6537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12824 Z= 0.301 Angle : 0.735 11.703 17426 Z= 0.363 Chirality : 0.050 0.379 1904 Planarity : 0.005 0.045 2235 Dihedral : 12.747 122.870 1966 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 29.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.98 % Favored : 91.96 % Rotamer: Outliers : 0.07 % Allowed : 1.71 % Favored : 98.22 % 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: -1.72 (0.20), residues: 1554 helix: -1.92 (0.42), residues: 132 sheet: -0.91 (0.28), residues: 309 loop : -1.16 (0.18), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 617 HIS 0.015 0.002 HIS A 160 PHE 0.017 0.002 PHE D 706 TYR 0.018 0.002 TYR E 84 ARG 0.006 0.001 ARG A 93 *********************** 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 63 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 62 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 229 LEU cc_start: 0.9300 (mm) cc_final: 0.8011 (tt) REVERT: E 293 GLU cc_start: 0.8837 (mt-10) cc_final: 0.7513 (mt-10) REVERT: E 294 MET cc_start: 0.9011 (mmm) cc_final: 0.8579 (mmm) REVERT: E 636 MET cc_start: 0.9021 (ttt) cc_final: 0.8751 (ttt) REVERT: D 223 MET cc_start: 0.7681 (tmm) cc_final: 0.7250 (tmm) REVERT: D 419 MET cc_start: 0.8488 (mtt) cc_final: 0.8155 (mtt) REVERT: D 579 LEU cc_start: 0.9363 (mt) cc_final: 0.9044 (mt) REVERT: D 686 MET cc_start: 0.9035 (ttp) cc_final: 0.8609 (tpp) outliers start: 1 outliers final: 0 residues processed: 62 average time/residue: 0.2316 time to fit residues: 23.6471 Evaluate side-chains 55 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 1.618 ------------------------------------------------------------------------------- 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: 8.9990 chunk 140 optimal weight: 10.0000 chunk 144 optimal weight: 7.9990 chunk 84 optimal weight: 8.9990 chunk 61 optimal weight: 7.9990 chunk 110 optimal weight: 9.9990 chunk 42 optimal weight: 1.9990 chunk 126 optimal weight: 20.0000 chunk 132 optimal weight: 6.9990 chunk 139 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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 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** D 95 GLN ** 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: 0.8051 moved from start: 0.6975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 12824 Z= 0.405 Angle : 0.812 12.151 17426 Z= 0.409 Chirality : 0.052 0.384 1904 Planarity : 0.006 0.046 2235 Dihedral : 12.377 125.873 1966 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 35.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.07 % Favored : 90.86 % Rotamer: Outliers : 0.07 % Allowed : 0.89 % Favored : 99.03 % 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: -1.92 (0.20), residues: 1554 helix: -1.61 (0.45), residues: 114 sheet: -1.23 (0.27), residues: 326 loop : -1.30 (0.18), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 617 HIS 0.019 0.002 HIS E 522 PHE 0.023 0.003 PHE D 706 TYR 0.018 0.002 TYR E 84 ARG 0.007 0.001 ARG A 93 *********************** 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 64 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 63 time to evaluate : 1.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 35 MET cc_start: 0.6961 (tpt) cc_final: 0.6666 (tpt) REVERT: E 229 LEU cc_start: 0.9342 (mm) cc_final: 0.8382 (tt) REVERT: E 292 MET cc_start: 0.9361 (ptm) cc_final: 0.8690 (ppp) REVERT: E 362 MET cc_start: 0.8989 (ppp) cc_final: 0.8772 (ppp) REVERT: E 636 MET cc_start: 0.8956 (ttt) cc_final: 0.8683 (ttt) REVERT: D 212 MET cc_start: 0.7073 (ttt) cc_final: 0.6735 (tpp) REVERT: D 223 MET cc_start: 0.7780 (tmm) cc_final: 0.7336 (tmm) REVERT: D 419 MET cc_start: 0.8353 (mtt) cc_final: 0.8060 (mtt) REVERT: D 579 LEU cc_start: 0.9346 (mt) cc_final: 0.9004 (mt) REVERT: D 686 MET cc_start: 0.8944 (ttp) cc_final: 0.8508 (tpp) outliers start: 1 outliers final: 0 residues processed: 63 average time/residue: 0.2213 time to fit residues: 22.5774 Evaluate side-chains 52 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 1.543 ------------------------------------------------------------------------------- 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: 4.9990 chunk 90 optimal weight: 4.9990 chunk 70 optimal weight: 10.0000 chunk 102 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 143 optimal weight: 7.9990 chunk 123 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 75 optimal weight: 8.9990 chunk 98 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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** ** E 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN ** 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: 0.8039 moved from start: 0.7203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 12824 Z= 0.329 Angle : 0.764 10.668 17426 Z= 0.382 Chirality : 0.051 0.365 1904 Planarity : 0.006 0.071 2235 Dihedral : 11.818 128.932 1966 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 31.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.43 % Favored : 91.51 % Rotamer: Outliers : 0.07 % Allowed : 0.67 % Favored : 99.26 % 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: -1.93 (0.20), residues: 1554 helix: -1.67 (0.44), residues: 114 sheet: -1.29 (0.27), residues: 320 loop : -1.29 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 528 HIS 0.008 0.002 HIS A 114 PHE 0.025 0.002 PHE E 374 TYR 0.016 0.002 TYR E 84 ARG 0.007 0.001 ARG A 93 ********************** 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 64 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 63 time to evaluate : 1.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 MET cc_start: 0.8712 (tmm) cc_final: 0.8415 (tmm) REVERT: E 35 MET cc_start: 0.6945 (tpt) cc_final: 0.6603 (tpt) REVERT: E 227 MET cc_start: 0.6764 (pmm) cc_final: 0.6169 (pmm) REVERT: E 229 LEU cc_start: 0.9262 (mm) cc_final: 0.7905 (tt) REVERT: E 292 MET cc_start: 0.9165 (ptm) cc_final: 0.8921 (ptm) REVERT: E 293 GLU cc_start: 0.8576 (mt-10) cc_final: 0.7851 (mt-10) REVERT: E 636 MET cc_start: 0.9088 (ttt) cc_final: 0.8809 (ttt) REVERT: D 212 MET cc_start: 0.6975 (ttt) cc_final: 0.6654 (tpp) REVERT: D 223 MET cc_start: 0.7773 (tmm) cc_final: 0.7291 (tmm) REVERT: D 419 MET cc_start: 0.8281 (mtt) cc_final: 0.7947 (mtt) REVERT: D 579 LEU cc_start: 0.9358 (mt) cc_final: 0.9036 (mt) REVERT: D 686 MET cc_start: 0.9010 (ttp) cc_final: 0.8573 (tpp) outliers start: 1 outliers final: 0 residues processed: 63 average time/residue: 0.2176 time to fit residues: 22.1730 Evaluate side-chains 51 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 1.652 ------------------------------------------------------------------------------- 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: 4.9990 chunk 37 optimal weight: 9.9990 chunk 114 optimal weight: 9.9990 chunk 18 optimal weight: 8.9990 chunk 34 optimal weight: 9.9990 chunk 123 optimal weight: 30.0000 chunk 51 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 108 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 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 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 HIS ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.036391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.027846 restraints weight = 174154.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.028528 restraints weight = 119224.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.029016 restraints weight = 88609.011| |-----------------------------------------------------------------------------| r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.7381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 12824 Z= 0.325 Angle : 0.755 9.825 17426 Z= 0.377 Chirality : 0.051 0.355 1904 Planarity : 0.005 0.065 2235 Dihedral : 11.533 131.892 1966 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 31.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % 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: -1.93 (0.20), residues: 1554 helix: -1.52 (0.45), residues: 116 sheet: -1.24 (0.27), residues: 317 loop : -1.33 (0.18), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 528 HIS 0.008 0.002 HIS A 114 PHE 0.018 0.002 PHE D 706 TYR 0.018 0.002 TYR E 84 ARG 0.007 0.001 ARG A 93 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2147.59 seconds wall clock time: 41 minutes 51.66 seconds (2511.66 seconds total)