Starting phenix.real_space_refine on Tue Nov 14 22:29:48 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mo9_23921/11_2023/7mo9_23921_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mo9_23921/11_2023/7mo9_23921.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mo9_23921/11_2023/7mo9_23921.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mo9_23921/11_2023/7mo9_23921.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mo9_23921/11_2023/7mo9_23921_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mo9_23921/11_2023/7mo9_23921_updated.pdb" } resolution = 4.0 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 91 5.16 5 C 6134 2.51 5 N 1682 2.21 5 O 1848 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" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 9755 Number of models: 1 Model: "" Number of chains: 4 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: "D" Number of atoms: 2287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2287 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 16, 'TRANS': 288} Chain breaks: 2 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 117 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 83 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: "B" 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: 5.72, per 1000 atoms: 0.59 Number of scatterers: 9755 At special positions: 0 Unit cell: (123.12, 137.16, 108, 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 91 16.00 O 1848 8.00 N 1682 7.00 C 6134 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=29, symmetry=0 Simple disulfide: pdb=" SG CYS A 70 " - pdb=" SG CYS A 96 " distance=2.05 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS A 84 " distance=2.04 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 206 " distance=2.02 Simple disulfide: pdb=" SG CYS A 149 " - pdb=" SG CYS A 189 " distance=2.03 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 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=2.04 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=2.04 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=2.01 Simple disulfide: pdb=" SG CYS E 172 " - pdb=" SG CYS E 175 " distance=2.04 Simple disulfide: pdb=" SG CYS E 282 " - pdb=" SG CYS E 409 " distance=2.03 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=2.03 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=2.03 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=2.04 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 B 2 " - " SGN B 3 " " IDS B 4 " - " SGN B 5 " BETA1-4 " SGN B 1 " - " IDS B 2 " ~> Even though IDS is an alpha isomer, a beta linkage is required... " SGN B 3 " - " IDS B 4 " " SGN B 5 " - " IDS B 6 " Time building additional restraints: 4.62 Conformation dependent library (CDL) restraints added in 1.7 seconds 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2322 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 18 helices and 23 sheets defined 8.3% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.30 Creating SS restraints... Processing helix chain 'A' and resid 67 through 75 Processing helix chain 'A' and resid 124 through 126 No H-bonds generated for 'chain 'A' and resid 124 through 126' Processing helix chain 'A' and resid 162 through 166 Processing helix chain 'A' and resid 207 through 209 No H-bonds generated for 'chain 'A' and resid 207 through 209' 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: 5.467A pdb=" N LYS D 714 " --> pdb=" O TYR D 711 " (cutoff:3.500A) 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: 3.676A 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 380 through 382 No H-bonds generated for 'chain 'E' and resid 380 through 382' 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 396 through 398 No H-bonds generated for 'chain 'E' and resid 396 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 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 61 through 63 removed outlier: 3.977A pdb=" N LYS A 62 " --> pdb=" O CYS A 96 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N CYS A 96 " --> pdb=" O LYS A 62 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLN A 95 " --> pdb=" O ASP A 90 " (cutoff:3.500A) removed outlier: 3.776A 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 'D' and resid 563 through 565 removed outlier: 3.879A pdb=" N CYS D 519 " --> pdb=" O LEU D 511 " (cutoff:3.500A) removed outlier: 8.839A 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: 6.622A pdb=" N TRP D 528 " --> pdb=" O ILE D 524 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 630 through 632 removed outlier: 3.504A pdb=" N SER D 613 " --> pdb=" O VAL D 678 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL D 678 " --> pdb=" O SER D 613 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N TYR D 615 " --> pdb=" O PRO D 676 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N CYS D 679 " --> pdb=" O VAL D 687 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N VAL D 687 " --> pdb=" O CYS D 679 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL D 707 " --> pdb=" O VAL D 690 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 45 through 47 Processing sheet with id= I, first strand: chain 'E' and resid 52 through 58 removed outlier: 6.857A 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: 6.931A 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: 6.946A pdb=" N HIS E 61 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA E 82 " --> pdb=" O VAL E 72 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 89 through 91 Processing sheet with id= K, first strand: chain 'E' and resid 119 through 123 removed outlier: 3.630A pdb=" N ALA E 119 " --> pdb=" O CYS E 133 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 182 through 188 Processing sheet with id= M, first strand: chain 'E' and resid 292 through 295 removed outlier: 6.536A pdb=" N VAL E 264 " --> pdb=" O TYR E 249 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N TYR E 249 " --> pdb=" O VAL E 264 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 424 through 427 removed outlier: 4.046A pdb=" N CYS E 298 " --> pdb=" O PHE E 314 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 360 through 366 removed outlier: 3.538A pdb=" N ALA E 319 " --> pdb=" O VAL E 345 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ALA E 347 " --> pdb=" O LEU E 317 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N LEU E 317 " --> pdb=" O ALA E 347 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 444 through 447 Processing sheet with id= Q, first strand: chain 'E' and resid 461 through 464 removed outlier: 4.314A 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= R, first strand: chain 'E' and resid 538 through 540 Processing sheet with id= S, first strand: chain 'E' and resid 621 through 625 removed outlier: 6.657A 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= T, first strand: chain 'E' and resid 601 through 605 Processing sheet with id= U, first strand: chain 'E' and resid 658 through 663 removed outlier: 6.731A pdb=" N THR E 678 " --> pdb=" O THR E 660 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ILE E 662 " --> pdb=" O THR E 676 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N THR E 676 " --> pdb=" O ILE E 662 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N TYR E 710 " --> pdb=" O LEU E 699 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU E 699 " --> pdb=" O TYR E 710 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 689 through 691 removed outlier: 4.110A pdb=" N SER E 691 " --> pdb=" O LYS E 723 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LYS E 723 " --> pdb=" O SER E 691 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 719 through 721 removed outlier: 3.956A pdb=" N PHE E 720 " --> pdb=" O PHE E 736 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE E 736 " --> pdb=" O PHE E 720 " (cutoff:3.500A) No H-bonds generated for sheet with id= W 200 hydrogen bonds defined for protein. 501 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: 3.11 Time building geometry restraints manager: 4.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3160 1.34 - 1.46: 2364 1.46 - 1.59: 4358 1.59 - 1.71: 3 1.71 - 1.83: 105 Bond restraints: 9990 Sorted by residual: bond pdb=" O6 SGN B 1 " pdb=" S2 SGN B 1 " ideal model delta sigma weight residual 1.660 1.530 0.130 2.00e-02 2.50e+03 4.20e+01 bond pdb=" CA THR E 86 " pdb=" CB THR E 86 " ideal model delta sigma weight residual 1.526 1.432 0.094 1.49e-02 4.50e+03 3.99e+01 bond pdb=" O2 IDS B 4 " pdb=" S IDS B 4 " ideal model delta sigma weight residual 1.646 1.521 0.125 2.00e-02 2.50e+03 3.91e+01 bond pdb=" O6 SGN B 3 " pdb=" S2 SGN B 3 " ideal model delta sigma weight residual 1.660 1.551 0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" O2 IDS B 2 " pdb=" S IDS B 2 " ideal model delta sigma weight residual 1.646 1.544 0.102 2.00e-02 2.50e+03 2.61e+01 ... (remaining 9985 not shown) Histogram of bond angle deviations from ideal: 98.06 - 105.31: 235 105.31 - 112.57: 5138 112.57 - 119.82: 3348 119.82 - 127.07: 4716 127.07 - 134.32: 140 Bond angle restraints: 13577 Sorted by residual: angle pdb=" C CYS E 561 " pdb=" N LEU E 562 " pdb=" CA LEU E 562 " ideal model delta sigma weight residual 120.49 131.10 -10.61 1.42e+00 4.96e-01 5.58e+01 angle pdb=" CB ARG E 413 " pdb=" CG ARG E 413 " pdb=" CD ARG E 413 " ideal model delta sigma weight residual 111.30 98.06 13.24 2.30e+00 1.89e-01 3.31e+01 angle pdb=" CA ARG E 218 " pdb=" CB ARG E 218 " pdb=" CG ARG E 218 " ideal model delta sigma weight residual 114.10 104.46 9.64 2.00e+00 2.50e-01 2.32e+01 angle pdb=" CB ARG D 695 " pdb=" CG ARG D 695 " pdb=" CD ARG D 695 " ideal model delta sigma weight residual 111.30 121.70 -10.40 2.30e+00 1.89e-01 2.05e+01 angle pdb=" CA VAL D 692 " pdb=" C VAL D 692 " pdb=" N PRO D 693 " ideal model delta sigma weight residual 116.57 120.87 -4.30 9.80e-01 1.04e+00 1.93e+01 ... (remaining 13572 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 5145 17.99 - 35.97: 676 35.97 - 53.96: 122 53.96 - 71.95: 19 71.95 - 89.94: 12 Dihedral angle restraints: 5974 sinusoidal: 2368 harmonic: 3606 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 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 -172.07 86.07 1 1.00e+01 1.00e-02 8.94e+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 93.00 7.21 85.79 1 1.00e+01 1.00e-02 8.90e+01 ... (remaining 5971 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1022 0.055 - 0.109: 373 0.109 - 0.164: 94 0.164 - 0.219: 14 0.219 - 0.273: 5 Chirality restraints: 1508 Sorted by residual: chirality pdb=" C1 IDS B 4 " pdb=" O4 SGN B 3 " pdb=" C2 IDS B 4 " pdb=" O5 IDS B 4 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 5.08e+01 chirality pdb=" C1 IDS B 6 " pdb=" O4 SGN B 5 " pdb=" C2 IDS B 6 " pdb=" O5 IDS B 6 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 4.86e+01 chirality pdb=" C1 IDS B 2 " pdb=" O4 SGN B 1 " pdb=" C2 IDS B 2 " pdb=" O5 IDS B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.49 0.09 2.00e-02 2.50e+03 1.95e+01 ... (remaining 1505 not shown) Planarity restraints: 1744 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU A 159 " -0.017 2.00e-02 2.50e+03 3.52e-02 1.24e+01 pdb=" CD GLU A 159 " 0.061 2.00e-02 2.50e+03 pdb=" OE1 GLU A 159 " -0.022 2.00e-02 2.50e+03 pdb=" OE2 GLU A 159 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 192 " 0.031 2.00e-02 2.50e+03 2.63e-02 1.21e+01 pdb=" CG PHE E 192 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 PHE E 192 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE E 192 " -0.006 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 8.68e+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 ... (remaining 1741 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 207 2.57 - 3.15: 9090 3.15 - 3.73: 15281 3.73 - 4.32: 20870 4.32 - 4.90: 33226 Nonbonded interactions: 78674 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 A 36 " pdb=" ND2 ASN A 72 " model vdw 2.013 2.520 nonbonded pdb=" O ASN E 571 " pdb=" OG SER E 653 " model vdw 2.082 2.440 nonbonded pdb=" NE2 GLN E 232 " pdb=" OE2 GLU E 415 " model vdw 2.084 2.520 nonbonded pdb=" O PHE E 374 " pdb=" NH1 ARG E 404 " model vdw 2.085 2.520 ... (remaining 78669 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.070 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: 4.820 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 30.850 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 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 : 0.010 0.130 9990 Z= 0.657 Angle : 1.231 13.235 13577 Z= 0.663 Chirality : 0.060 0.273 1508 Planarity : 0.007 0.069 1744 Dihedral : 16.043 89.936 3565 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 34.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 0.38 % Allowed : 2.55 % Favored : 97.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -2.30 (0.22), residues: 1227 helix: -1.66 (0.54), residues: 83 sheet: -1.50 (0.27), residues: 317 loop : -1.58 (0.21), residues: 827 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 94 time to evaluate : 1.198 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 98 average time/residue: 0.2042 time to fit residues: 29.5041 Evaluate side-chains 76 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 75 time to evaluate : 1.191 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0888 time to fit residues: 1.7174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 chunk 96 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 233 GLN ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 GLN ** D 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 ASN ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 9990 Z= 0.303 Angle : 0.816 12.009 13577 Z= 0.412 Chirality : 0.050 0.227 1508 Planarity : 0.006 0.077 1744 Dihedral : 7.194 59.612 1346 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 24.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 1.61 % Allowed : 15.89 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -1.88 (0.23), residues: 1227 helix: -0.84 (0.59), residues: 69 sheet: -1.27 (0.28), residues: 293 loop : -1.33 (0.21), residues: 865 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 85 time to evaluate : 1.275 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 12 residues processed: 94 average time/residue: 0.1864 time to fit residues: 27.1770 Evaluate side-chains 84 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 72 time to evaluate : 1.387 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0991 time to fit residues: 3.8141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 111 optimal weight: 20.0000 chunk 120 optimal weight: 0.0370 chunk 99 optimal weight: 0.7980 chunk 110 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 HIS ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9990 Z= 0.192 Angle : 0.718 11.412 13577 Z= 0.355 Chirality : 0.048 0.218 1508 Planarity : 0.005 0.040 1744 Dihedral : 6.434 58.744 1346 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 18.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.51 % Allowed : 18.45 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -1.63 (0.23), residues: 1227 helix: -0.81 (0.56), residues: 81 sheet: -0.84 (0.29), residues: 284 loop : -1.24 (0.21), residues: 862 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 93 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 8 residues processed: 109 average time/residue: 0.1870 time to fit residues: 31.0513 Evaluate side-chains 91 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 83 time to evaluate : 1.096 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0869 time to fit residues: 2.7685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 9.9990 chunk 84 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 75 optimal weight: 0.9990 chunk 112 optimal weight: 8.9990 chunk 118 optimal weight: 30.0000 chunk 106 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 494 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 9990 Z= 0.292 Angle : 0.710 10.846 13577 Z= 0.354 Chirality : 0.048 0.200 1508 Planarity : 0.005 0.053 1744 Dihedral : 6.322 58.452 1346 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 21.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 2.65 % Allowed : 21.19 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -1.58 (0.23), residues: 1227 helix: -1.11 (0.56), residues: 82 sheet: -0.91 (0.29), residues: 294 loop : -1.13 (0.21), residues: 851 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 82 time to evaluate : 1.235 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 17 residues processed: 106 average time/residue: 0.1898 time to fit residues: 30.7638 Evaluate side-chains 96 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 79 time to evaluate : 1.194 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.0980 time to fit residues: 4.6540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 49 optimal weight: 8.9990 chunk 101 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 60 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 680 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 9990 Z= 0.362 Angle : 0.739 9.444 13577 Z= 0.369 Chirality : 0.049 0.196 1508 Planarity : 0.005 0.048 1744 Dihedral : 6.365 57.935 1346 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 23.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 1.99 % Allowed : 23.27 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -1.58 (0.23), residues: 1227 helix: -1.14 (0.63), residues: 69 sheet: -0.94 (0.29), residues: 289 loop : -1.12 (0.21), residues: 869 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 78 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 13 residues processed: 99 average time/residue: 0.1912 time to fit residues: 28.6202 Evaluate side-chains 87 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 74 time to evaluate : 1.355 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1243 time to fit residues: 4.3662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 119 optimal weight: 0.0370 chunk 98 optimal weight: 0.5980 chunk 55 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 chunk 114 optimal weight: 10.0000 overall best weight: 2.3264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 9990 Z= 0.260 Angle : 0.692 9.088 13577 Z= 0.343 Chirality : 0.047 0.200 1508 Planarity : 0.005 0.042 1744 Dihedral : 6.154 56.763 1346 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 20.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 2.37 % Allowed : 24.60 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -1.54 (0.23), residues: 1227 helix: -1.32 (0.58), residues: 77 sheet: -0.88 (0.29), residues: 288 loop : -1.07 (0.21), residues: 862 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 79 time to evaluate : 1.274 Fit side-chains outliers start: 25 outliers final: 13 residues processed: 100 average time/residue: 0.1854 time to fit residues: 29.0433 Evaluate side-chains 90 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 77 time to evaluate : 1.237 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1023 time to fit residues: 4.0740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 7.9990 chunk 67 optimal weight: 5.9990 chunk 86 optimal weight: 9.9990 chunk 100 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 74 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 9990 Z= 0.295 Angle : 0.700 8.888 13577 Z= 0.348 Chirality : 0.047 0.198 1508 Planarity : 0.005 0.044 1744 Dihedral : 6.123 56.369 1346 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 21.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 1.32 % Allowed : 25.83 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -1.54 (0.23), residues: 1227 helix: -1.29 (0.59), residues: 75 sheet: -0.95 (0.28), residues: 301 loop : -1.05 (0.21), residues: 851 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 78 time to evaluate : 1.196 Fit side-chains outliers start: 14 outliers final: 9 residues processed: 88 average time/residue: 0.1754 time to fit residues: 24.6055 Evaluate side-chains 85 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 76 time to evaluate : 1.206 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0930 time to fit residues: 3.1774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 75 optimal weight: 0.0970 chunk 80 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 11 optimal weight: 0.0970 chunk 93 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 113 optimal weight: 9.9990 overall best weight: 1.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 620 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9990 Z= 0.217 Angle : 0.679 9.100 13577 Z= 0.335 Chirality : 0.047 0.192 1508 Planarity : 0.005 0.046 1744 Dihedral : 5.956 55.354 1346 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 19.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.14 % Allowed : 26.11 % Favored : 72.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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 (0.23), residues: 1227 helix: -1.22 (0.60), residues: 73 sheet: -0.86 (0.28), residues: 301 loop : -1.00 (0.21), residues: 853 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 80 time to evaluate : 1.613 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 91 average time/residue: 0.1943 time to fit residues: 27.0869 Evaluate side-chains 80 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 74 time to evaluate : 1.177 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1896 time to fit residues: 3.1933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 5.9990 chunk 110 optimal weight: 8.9990 chunk 113 optimal weight: 8.9990 chunk 66 optimal weight: 0.0070 chunk 48 optimal weight: 20.0000 chunk 86 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 99 optimal weight: 8.9990 chunk 104 optimal weight: 0.9990 chunk 72 optimal weight: 0.5980 chunk 116 optimal weight: 10.0000 overall best weight: 1.5202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 645 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9990 Z= 0.210 Angle : 0.686 12.463 13577 Z= 0.334 Chirality : 0.047 0.188 1508 Planarity : 0.005 0.047 1744 Dihedral : 5.857 54.731 1346 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 19.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 0.95 % Allowed : 26.58 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -1.48 (0.23), residues: 1227 helix: -1.34 (0.58), residues: 73 sheet: -0.87 (0.28), residues: 304 loop : -1.01 (0.21), residues: 850 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 79 time to evaluate : 1.229 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 87 average time/residue: 0.1824 time to fit residues: 24.9249 Evaluate side-chains 80 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 75 time to evaluate : 1.195 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0945 time to fit residues: 2.4683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 1.9990 chunk 55 optimal weight: 9.9990 chunk 81 optimal weight: 5.9990 chunk 122 optimal weight: 9.9990 chunk 112 optimal weight: 0.0050 chunk 97 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 chunk 59 optimal weight: 8.9990 chunk 77 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 overall best weight: 1.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9990 Z= 0.212 Angle : 0.693 11.792 13577 Z= 0.337 Chirality : 0.047 0.189 1508 Planarity : 0.005 0.041 1744 Dihedral : 5.782 54.114 1346 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 19.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 0.38 % Allowed : 27.53 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -1.47 (0.23), residues: 1227 helix: -1.35 (0.56), residues: 79 sheet: -0.80 (0.28), residues: 304 loop : -1.02 (0.21), residues: 844 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 78 time to evaluate : 1.207 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 81 average time/residue: 0.1767 time to fit residues: 22.9922 Evaluate side-chains 80 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 78 time to evaluate : 1.306 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1192 time to fit residues: 1.9657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 97 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.076509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.058713 restraints weight = 43026.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.059713 restraints weight = 26280.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.060229 restraints weight = 19331.045| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 9990 Z= 0.267 Angle : 0.699 11.568 13577 Z= 0.342 Chirality : 0.047 0.192 1508 Planarity : 0.005 0.040 1744 Dihedral : 5.833 53.883 1346 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 20.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 0.38 % Allowed : 28.29 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -1.49 (0.23), residues: 1227 helix: -1.51 (0.57), residues: 74 sheet: -0.86 (0.28), residues: 304 loop : -1.00 (0.21), residues: 849 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1815.62 seconds wall clock time: 34 minutes 12.15 seconds (2052.15 seconds total)