Starting phenix.real_space_refine on Thu Mar 14 21:16:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mo9_23921/03_2024/7mo9_23921_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mo9_23921/03_2024/7mo9_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_23921/03_2024/7mo9_23921.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mo9_23921/03_2024/7mo9_23921.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mo9_23921/03_2024/7mo9_23921_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mo9_23921/03_2024/7mo9_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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 28 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 5.74, 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: 4.01 Conformation dependent library (CDL) restraints added in 1.8 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: 2.32 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: 2.89 Time building geometry restraints manager: 4.32 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 - 26.18: 5635 26.18 - 52.36: 401 52.36 - 78.54: 35 78.54 - 104.72: 20 104.72 - 130.90: 6 Dihedral angle restraints: 6097 sinusoidal: 2491 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 6094 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: 0.780 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: 4.550 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 30.020 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.650 ------------------------------------------------------------------------------- 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 : 17.885 130.900 3688 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.004 TRP D 547 HIS 0.027 0.003 HIS E 275 PHE 0.057 0.004 PHE E 192 TYR 0.021 0.003 TYR E 501 ARG 0.048 0.003 ARG E 426 *********************** 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 : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 TRP cc_start: 0.6313 (m-10) cc_final: 0.5899 (m-10) REVERT: A 255 PHE cc_start: 0.7025 (m-10) cc_final: 0.6780 (m-80) REVERT: A 258 ASN cc_start: 0.7065 (OUTLIER) cc_final: 0.6852 (m110) REVERT: E 463 MET cc_start: 0.8530 (mtm) cc_final: 0.8311 (mtt) REVERT: E 591 ARG cc_start: 0.6741 (ttt-90) cc_final: 0.6512 (mtp85) outliers start: 4 outliers final: 1 residues processed: 98 average time/residue: 0.1982 time to fit residues: 28.4790 Evaluate side-chains 80 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 78 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain E residue 594 ASN 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: 1.9990 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: 2.5990 ------------------------------------------------------------------------------- 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 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: 0.8083 moved from start: 0.1020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 9990 Z= 0.311 Angle : 0.824 11.951 13577 Z= 0.413 Chirality : 0.051 0.286 1508 Planarity : 0.006 0.083 1744 Dihedral : 12.706 107.945 1473 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 24.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 1.89 % Allowed : 15.89 % Favored : 82.21 % 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: -0.81 (0.60), residues: 69 sheet: -1.28 (0.28), residues: 293 loop : -1.32 (0.21), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 547 HIS 0.019 0.002 HIS E 275 PHE 0.038 0.002 PHE E 192 TYR 0.018 0.002 TYR E 84 ARG 0.013 0.001 ARG D 695 *********************** 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 106 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 86 time to evaluate : 1.197 Fit side-chains revert: symmetry clash REVERT: A 279 ARG cc_start: 0.8219 (mmm-85) cc_final: 0.7606 (ptm160) outliers start: 20 outliers final: 12 residues processed: 98 average time/residue: 0.1826 time to fit residues: 26.8562 Evaluate side-chains 86 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 74 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain D residue 545 GLU Chi-restraints excluded: chain D residue 561 CYS Chi-restraints excluded: chain D residue 625 TYR Chi-restraints excluded: chain D residue 669 CYS Chi-restraints excluded: chain E residue 38 ASN Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 382 ASN Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain E residue 675 LEU Chi-restraints excluded: chain E residue 709 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 0.0270 chunk 34 optimal weight: 7.9990 chunk 92 optimal weight: 0.0670 chunk 76 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 111 optimal weight: 20.0000 chunk 120 optimal weight: 0.5980 chunk 99 optimal weight: 7.9990 chunk 110 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 overall best weight: 1.1378 ------------------------------------------------------------------------------- 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** ** 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** E 594 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9990 Z= 0.207 Angle : 0.734 11.414 13577 Z= 0.361 Chirality : 0.049 0.363 1508 Planarity : 0.005 0.043 1744 Dihedral : 11.270 105.857 1469 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 19.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 2.65 % Allowed : 18.64 % Favored : 78.71 % 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: -1.67 (0.23), residues: 1227 helix: -0.89 (0.57), residues: 75 sheet: -0.91 (0.29), residues: 290 loop : -1.25 (0.21), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 98 HIS 0.013 0.001 HIS E 275 PHE 0.014 0.001 PHE E 192 TYR 0.020 0.002 TYR A 259 ARG 0.007 0.001 ARG D 695 *********************** 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 116 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 88 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.8011 (mmtm) REVERT: A 274 LEU cc_start: 0.8496 (pt) cc_final: 0.8212 (mt) REVERT: D 415 TRP cc_start: 0.6831 (t-100) cc_final: 0.6372 (t-100) REVERT: D 581 LEU cc_start: 0.9070 (mm) cc_final: 0.8613 (mm) REVERT: D 644 GLN cc_start: 0.7969 (mm-40) cc_final: 0.7439 (mm110) REVERT: E 622 LEU cc_start: 0.9288 (mm) cc_final: 0.9045 (mm) outliers start: 28 outliers final: 18 residues processed: 110 average time/residue: 0.2381 time to fit residues: 39.1302 Evaluate side-chains 97 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 78 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 223 MET Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain D residue 561 CYS Chi-restraints excluded: chain D residue 625 TYR Chi-restraints excluded: chain D residue 669 CYS Chi-restraints excluded: chain E residue 129 GLN Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 492 VAL Chi-restraints excluded: chain E residue 571 ASN Chi-restraints excluded: chain E residue 594 ASN Chi-restraints excluded: chain E residue 603 VAL Chi-restraints excluded: chain E residue 675 LEU Chi-restraints excluded: chain E residue 709 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 20.0000 chunk 84 optimal weight: 6.9990 chunk 58 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 chunk 75 optimal weight: 0.0370 chunk 112 optimal weight: 8.9990 chunk 118 optimal weight: 30.0000 chunk 106 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 99 optimal weight: 8.9990 overall best weight: 2.7464 ------------------------------------------------------------------------------- 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** ** 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 494 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 9990 Z= 0.299 Angle : 0.723 10.962 13577 Z= 0.356 Chirality : 0.049 0.353 1508 Planarity : 0.005 0.052 1744 Dihedral : 10.508 105.238 1469 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 21.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 4.26 % Allowed : 19.96 % Favored : 75.78 % 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: -1.66 (0.23), residues: 1227 helix: -1.08 (0.57), residues: 82 sheet: -1.00 (0.28), residues: 295 loop : -1.17 (0.21), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 98 HIS 0.012 0.001 HIS E 275 PHE 0.010 0.001 PHE E 192 TYR 0.015 0.002 TYR A 259 ARG 0.006 0.001 ARG D 695 *********************** 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 124 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 79 time to evaluate : 1.340 Fit side-chains revert: symmetry clash REVERT: A 110 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.7967 (mmtm) REVERT: A 255 PHE cc_start: 0.7136 (m-10) cc_final: 0.6852 (m-80) REVERT: A 274 LEU cc_start: 0.8556 (pt) cc_final: 0.8224 (mt) REVERT: D 415 TRP cc_start: 0.6783 (t-100) cc_final: 0.6327 (t-100) REVERT: D 644 GLN cc_start: 0.7939 (mm-40) cc_final: 0.7487 (mm110) REVERT: D 686 MET cc_start: 0.7700 (ttp) cc_final: 0.7454 (ttm) REVERT: E 40 LYS cc_start: 0.7923 (OUTLIER) cc_final: 0.7686 (mtmm) outliers start: 45 outliers final: 29 residues processed: 119 average time/residue: 0.1668 time to fit residues: 30.6283 Evaluate side-chains 106 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 75 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain D residue 561 CYS Chi-restraints excluded: chain D residue 589 VAL Chi-restraints excluded: chain D residue 625 TYR Chi-restraints excluded: chain D residue 669 CYS Chi-restraints excluded: chain D residue 692 VAL Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain E residue 40 LYS Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 129 GLN Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 382 ASN Chi-restraints excluded: chain E residue 418 THR Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 451 THR Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain E residue 492 VAL Chi-restraints excluded: chain E residue 506 THR Chi-restraints excluded: chain E residue 568 VAL Chi-restraints excluded: chain E residue 571 ASN Chi-restraints excluded: chain E residue 603 VAL Chi-restraints excluded: chain E residue 709 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 49 optimal weight: 0.0970 chunk 101 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 60 optimal weight: 3.9990 chunk 106 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- 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** ** D 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 ASN E 58 HIS ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 594 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2140 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= 0.220 Angle : 0.695 10.516 13577 Z= 0.338 Chirality : 0.048 0.330 1508 Planarity : 0.005 0.042 1744 Dihedral : 9.793 102.975 1469 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 18.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 3.97 % Allowed : 22.14 % Favored : 73.89 % 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: -1.52 (0.23), residues: 1227 helix: -1.34 (0.56), residues: 77 sheet: -0.78 (0.30), residues: 283 loop : -1.09 (0.21), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 98 HIS 0.011 0.001 HIS E 275 PHE 0.011 0.001 PHE E 192 TYR 0.017 0.002 TYR A 272 ARG 0.006 0.001 ARG D 695 *********************** 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 126 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 84 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 255 PHE cc_start: 0.7241 (m-10) cc_final: 0.6989 (m-80) REVERT: A 274 LEU cc_start: 0.8670 (pt) cc_final: 0.8301 (mt) REVERT: D 415 TRP cc_start: 0.6706 (t-100) cc_final: 0.6247 (t-100) REVERT: D 534 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.8512 (mm110) REVERT: D 644 GLN cc_start: 0.7926 (mm-40) cc_final: 0.7508 (mm-40) REVERT: D 670 GLU cc_start: 0.7119 (mm-30) cc_final: 0.6903 (tp30) REVERT: D 686 MET cc_start: 0.7700 (ttp) cc_final: 0.7496 (ttm) REVERT: E 40 LYS cc_start: 0.7846 (OUTLIER) cc_final: 0.7622 (mtmm) outliers start: 42 outliers final: 29 residues processed: 123 average time/residue: 0.1851 time to fit residues: 34.2053 Evaluate side-chains 107 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 76 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain D residue 534 GLN Chi-restraints excluded: chain D residue 561 CYS Chi-restraints excluded: chain D residue 625 TYR Chi-restraints excluded: chain D residue 669 CYS Chi-restraints excluded: chain D residue 692 VAL Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain E residue 38 ASN Chi-restraints excluded: chain E residue 40 LYS Chi-restraints excluded: chain E residue 129 GLN Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 382 ASN Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain E residue 492 VAL Chi-restraints excluded: chain E residue 506 THR Chi-restraints excluded: chain E residue 516 ASN Chi-restraints excluded: chain E residue 524 GLN Chi-restraints excluded: chain E residue 555 THR Chi-restraints excluded: chain E residue 568 VAL Chi-restraints excluded: chain E residue 571 ASN Chi-restraints excluded: chain E residue 603 VAL Chi-restraints excluded: chain E residue 709 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 5.9990 chunk 23 optimal weight: 0.0470 chunk 69 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 119 optimal weight: 30.0000 chunk 98 optimal weight: 8.9990 chunk 55 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 114 optimal weight: 9.9990 overall best weight: 3.6084 ------------------------------------------------------------------------------- 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** ** 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 594 ASN E 680 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2175 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= 0.357 Angle : 0.731 10.242 13577 Z= 0.361 Chirality : 0.049 0.341 1508 Planarity : 0.005 0.042 1744 Dihedral : 9.676 101.598 1469 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 22.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 4.92 % Allowed : 22.23 % 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: -1.61 (0.23), residues: 1227 helix: -1.30 (0.59), residues: 75 sheet: -0.98 (0.28), residues: 295 loop : -1.11 (0.21), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 98 HIS 0.011 0.001 HIS E 275 PHE 0.012 0.002 PHE D 536 TYR 0.014 0.002 TYR A 272 ARG 0.007 0.001 ARG D 695 *********************** 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 124 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 72 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 LYS cc_start: 0.7663 (OUTLIER) cc_final: 0.7356 (mmtm) REVERT: A 255 PHE cc_start: 0.7291 (m-10) cc_final: 0.7061 (m-80) REVERT: A 274 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8330 (mt) REVERT: D 415 TRP cc_start: 0.6687 (t-100) cc_final: 0.6227 (t-100) REVERT: D 534 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.8542 (mm110) REVERT: D 644 GLN cc_start: 0.7961 (mm-40) cc_final: 0.7561 (mm110) REVERT: D 686 MET cc_start: 0.7769 (ttp) cc_final: 0.7539 (ttm) outliers start: 52 outliers final: 43 residues processed: 120 average time/residue: 0.1890 time to fit residues: 35.1402 Evaluate side-chains 117 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 71 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 503 THR Chi-restraints excluded: chain D residue 511 LEU Chi-restraints excluded: chain D residue 534 GLN Chi-restraints excluded: chain D residue 561 CYS Chi-restraints excluded: chain D residue 589 VAL Chi-restraints excluded: chain D residue 625 TYR Chi-restraints excluded: chain D residue 669 CYS Chi-restraints excluded: chain D residue 682 HIS Chi-restraints excluded: chain D residue 692 VAL Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain E residue 38 ASN Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 129 GLN Chi-restraints excluded: chain E residue 172 CYS Chi-restraints excluded: chain E residue 174 ASP Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 315 ASN Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 382 ASN Chi-restraints excluded: chain E residue 418 THR Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 451 THR Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain E residue 492 VAL Chi-restraints excluded: chain E residue 506 THR Chi-restraints excluded: chain E residue 524 GLN Chi-restraints excluded: chain E residue 555 THR Chi-restraints excluded: chain E residue 568 VAL Chi-restraints excluded: chain E residue 571 ASN Chi-restraints excluded: chain E residue 594 ASN Chi-restraints excluded: chain E residue 603 VAL Chi-restraints excluded: chain E residue 709 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 6.9990 chunk 67 optimal weight: 7.9990 chunk 86 optimal weight: 0.8980 chunk 100 optimal weight: 0.3980 chunk 66 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 72 optimal weight: 0.0040 chunk 54 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- 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** ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9990 Z= 0.169 Angle : 0.680 9.978 13577 Z= 0.329 Chirality : 0.048 0.312 1508 Planarity : 0.005 0.042 1744 Dihedral : 9.151 98.081 1469 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 18.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 4.16 % Allowed : 24.03 % Favored : 71.81 % 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: -1.42 (0.23), residues: 1227 helix: -1.16 (0.59), residues: 75 sheet: -0.71 (0.29), residues: 287 loop : -1.04 (0.21), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 98 HIS 0.012 0.001 HIS E 275 PHE 0.010 0.001 PHE E 241 TYR 0.016 0.001 TYR A 272 ARG 0.005 0.000 ARG E 592 *********************** 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 123 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 79 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 274 LEU cc_start: 0.8587 (pt) cc_final: 0.8263 (mt) REVERT: D 415 TRP cc_start: 0.6563 (t-100) cc_final: 0.6114 (t-100) REVERT: D 644 GLN cc_start: 0.8030 (mm-40) cc_final: 0.7622 (mm-40) REVERT: E 40 LYS cc_start: 0.7800 (OUTLIER) cc_final: 0.7586 (mtmm) REVERT: E 267 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7899 (mt-10) outliers start: 44 outliers final: 28 residues processed: 119 average time/residue: 0.1695 time to fit residues: 31.0720 Evaluate side-chains 106 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 76 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain D residue 503 THR Chi-restraints excluded: chain D residue 561 CYS Chi-restraints excluded: chain D residue 589 VAL Chi-restraints excluded: chain D residue 625 TYR Chi-restraints excluded: chain D residue 669 CYS Chi-restraints excluded: chain D residue 692 VAL Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain E residue 40 LYS Chi-restraints excluded: chain E residue 98 CYS Chi-restraints excluded: chain E residue 174 ASP Chi-restraints excluded: chain E residue 267 GLU Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 382 ASN Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 451 THR Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain E residue 506 THR Chi-restraints excluded: chain E residue 516 ASN Chi-restraints excluded: chain E residue 524 GLN Chi-restraints excluded: chain E residue 568 VAL Chi-restraints excluded: chain E residue 571 ASN Chi-restraints excluded: chain E residue 603 VAL Chi-restraints excluded: chain E residue 709 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 9.9990 chunk 35 optimal weight: 7.9990 chunk 23 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 80 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 93 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 chunk 113 optimal weight: 8.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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** ** D 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 534 GLN ** 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 620 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9990 Z= 0.259 Angle : 0.693 9.974 13577 Z= 0.337 Chirality : 0.048 0.308 1508 Planarity : 0.005 0.039 1744 Dihedral : 8.981 95.886 1469 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 20.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 4.54 % Allowed : 23.84 % Favored : 71.62 % 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: -1.42 (0.23), residues: 1227 helix: -1.28 (0.56), residues: 81 sheet: -0.76 (0.29), residues: 288 loop : -0.99 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 98 HIS 0.011 0.001 HIS E 275 PHE 0.019 0.001 PHE E 430 TYR 0.012 0.001 TYR A 272 ARG 0.005 0.001 ARG E 218 *********************** 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 122 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 74 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 415 TRP cc_start: 0.6552 (t-100) cc_final: 0.6128 (t-100) REVERT: D 644 GLN cc_start: 0.8035 (mm-40) cc_final: 0.7618 (mm-40) REVERT: E 40 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7769 (mtmm) REVERT: E 267 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7704 (mt-10) outliers start: 48 outliers final: 36 residues processed: 118 average time/residue: 0.1748 time to fit residues: 31.5582 Evaluate side-chains 111 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 73 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 272 TYR Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 503 THR Chi-restraints excluded: chain D residue 561 CYS Chi-restraints excluded: chain D residue 589 VAL Chi-restraints excluded: chain D residue 625 TYR Chi-restraints excluded: chain D residue 669 CYS Chi-restraints excluded: chain D residue 682 HIS Chi-restraints excluded: chain D residue 692 VAL Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain E residue 38 ASN Chi-restraints excluded: chain E residue 40 LYS Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 98 CYS Chi-restraints excluded: chain E residue 129 GLN Chi-restraints excluded: chain E residue 172 CYS Chi-restraints excluded: chain E residue 174 ASP Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 267 GLU Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 382 ASN Chi-restraints excluded: chain E residue 409 CYS Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 451 THR Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain E residue 506 THR Chi-restraints excluded: chain E residue 516 ASN Chi-restraints excluded: chain E residue 524 GLN Chi-restraints excluded: chain E residue 568 VAL Chi-restraints excluded: chain E residue 571 ASN Chi-restraints excluded: chain E residue 603 VAL Chi-restraints excluded: chain E residue 709 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 2.9990 chunk 110 optimal weight: 10.0000 chunk 113 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 chunk 48 optimal weight: 20.0000 chunk 86 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 chunk 104 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 116 optimal weight: 20.0000 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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** ** D 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 534 GLN ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9990 Z= 0.246 Angle : 0.706 11.726 13577 Z= 0.341 Chirality : 0.048 0.303 1508 Planarity : 0.005 0.040 1744 Dihedral : 8.861 93.872 1469 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 19.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 4.07 % Allowed : 24.50 % Favored : 71.43 % 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: -1.44 (0.23), residues: 1227 helix: -1.40 (0.56), residues: 75 sheet: -0.76 (0.29), residues: 288 loop : -1.01 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 98 HIS 0.011 0.001 HIS E 275 PHE 0.017 0.001 PHE E 241 TYR 0.013 0.001 TYR A 272 ARG 0.006 0.001 ARG E 218 *********************** 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 117 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 74 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 274 LEU cc_start: 0.8710 (pt) cc_final: 0.8311 (mt) REVERT: D 415 TRP cc_start: 0.6522 (t-100) cc_final: 0.6088 (t-100) REVERT: D 644 GLN cc_start: 0.8056 (mm-40) cc_final: 0.7665 (mm-40) REVERT: E 40 LYS cc_start: 0.7975 (OUTLIER) cc_final: 0.7759 (mtmm) REVERT: E 267 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7685 (mt-10) outliers start: 43 outliers final: 40 residues processed: 113 average time/residue: 0.1689 time to fit residues: 29.5819 Evaluate side-chains 117 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 75 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 272 TYR Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 503 THR Chi-restraints excluded: chain D residue 511 LEU Chi-restraints excluded: chain D residue 561 CYS Chi-restraints excluded: chain D residue 589 VAL Chi-restraints excluded: chain D residue 625 TYR Chi-restraints excluded: chain D residue 669 CYS Chi-restraints excluded: chain D residue 682 HIS Chi-restraints excluded: chain D residue 692 VAL Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain E residue 40 LYS Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 98 CYS Chi-restraints excluded: chain E residue 129 GLN Chi-restraints excluded: chain E residue 172 CYS Chi-restraints excluded: chain E residue 174 ASP Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 267 GLU Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 315 ASN Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 382 ASN Chi-restraints excluded: chain E residue 409 CYS Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 451 THR Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain E residue 506 THR Chi-restraints excluded: chain E residue 510 ILE Chi-restraints excluded: chain E residue 516 ASN Chi-restraints excluded: chain E residue 524 GLN Chi-restraints excluded: chain E residue 568 VAL Chi-restraints excluded: chain E residue 571 ASN Chi-restraints excluded: chain E residue 603 VAL Chi-restraints excluded: chain E residue 709 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 81 optimal weight: 6.9990 chunk 122 optimal weight: 9.9990 chunk 112 optimal weight: 0.4980 chunk 97 optimal weight: 0.7980 chunk 10 optimal weight: 9.9990 chunk 75 optimal weight: 0.9980 chunk 59 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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** ** D 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 534 GLN ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9990 Z= 0.168 Angle : 0.691 12.235 13577 Z= 0.327 Chirality : 0.047 0.269 1508 Planarity : 0.004 0.038 1744 Dihedral : 8.277 86.797 1469 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 3.41 % Allowed : 25.64 % Favored : 70.96 % 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: -1.40 (0.23), residues: 1227 helix: -1.11 (0.56), residues: 75 sheet: -0.68 (0.28), residues: 305 loop : -1.03 (0.21), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 98 HIS 0.011 0.001 HIS E 275 PHE 0.011 0.001 PHE D 536 TYR 0.013 0.001 TYR D 619 ARG 0.004 0.001 ARG E 218 ********************** 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 118 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 82 time to evaluate : 1.057 Fit side-chains REVERT: A 274 LEU cc_start: 0.8841 (pt) cc_final: 0.8305 (mt) REVERT: D 415 TRP cc_start: 0.6644 (t-100) cc_final: 0.6230 (t-100) REVERT: D 644 GLN cc_start: 0.8111 (mm-40) cc_final: 0.7791 (mm-40) REVERT: E 267 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7853 (mt-10) REVERT: E 569 PHE cc_start: 0.8329 (m-80) cc_final: 0.8114 (m-80) REVERT: E 590 PHE cc_start: 0.7897 (t80) cc_final: 0.7360 (t80) outliers start: 36 outliers final: 30 residues processed: 115 average time/residue: 0.1650 time to fit residues: 29.4340 Evaluate side-chains 106 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 75 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 503 THR Chi-restraints excluded: chain D residue 561 CYS Chi-restraints excluded: chain D residue 589 VAL Chi-restraints excluded: chain D residue 625 TYR Chi-restraints excluded: chain D residue 692 VAL Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain E residue 38 ASN Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 98 CYS Chi-restraints excluded: chain E residue 172 CYS Chi-restraints excluded: chain E residue 174 ASP Chi-restraints excluded: chain E residue 267 GLU Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 382 ASN Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 451 THR Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain E residue 506 THR Chi-restraints excluded: chain E residue 510 ILE Chi-restraints excluded: chain E residue 516 ASN Chi-restraints excluded: chain E residue 524 GLN Chi-restraints excluded: chain E residue 568 VAL Chi-restraints excluded: chain E residue 603 VAL Chi-restraints excluded: chain E residue 709 CYS 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: 4.9990 chunk 14 optimal weight: 0.8980 chunk 27 optimal weight: 10.0000 chunk 97 optimal weight: 9.9990 chunk 40 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 12 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 85 optimal weight: 4.9990 chunk 5 optimal weight: 10.0000 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 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 285 ASN ** 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 = 0.3559 r_free = 0.3559 target = 0.077457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.059074 restraints weight = 42770.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.060510 restraints weight = 26287.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.061442 restraints weight = 18901.867| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.129 9990 Z= 0.257 Angle : 0.966 59.194 13577 Z= 0.531 Chirality : 0.053 0.862 1508 Planarity : 0.005 0.042 1744 Dihedral : 8.306 86.756 1469 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 19.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.62 % Favored : 94.30 % Rotamer: Outliers : 2.93 % Allowed : 26.77 % Favored : 70.29 % Cbeta Deviations : 0.09 % 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: -1.41 (0.23), residues: 1227 helix: -1.18 (0.56), residues: 75 sheet: -0.67 (0.28), residues: 305 loop : -1.04 (0.21), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 98 HIS 0.010 0.001 HIS E 275 PHE 0.034 0.001 PHE E 430 TYR 0.013 0.001 TYR D 619 ARG 0.003 0.000 ARG D 695 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1852.87 seconds wall clock time: 34 minutes 37.75 seconds (2077.75 seconds total)