Starting phenix.real_space_refine on Tue Jun 25 16:29:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpb_16148/06_2024/8bpb_16148_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpb_16148/06_2024/8bpb_16148.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpb_16148/06_2024/8bpb_16148.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpb_16148/06_2024/8bpb_16148.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpb_16148/06_2024/8bpb_16148_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpb_16148/06_2024/8bpb_16148_neut_updated.pdb" } resolution = 2.8 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= 0.004 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: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 Zn 3 6.06 5 S 55 5.16 5 C 5329 2.51 5 N 1447 2.21 5 O 1548 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 322": "OE1" <-> "OE2" Residue "A GLU 325": "OE1" <-> "OE2" Residue "A GLU 449": "OE1" <-> "OE2" Residue "A GLU 461": "OE1" <-> "OE2" Residue "A GLU 467": "OE1" <-> "OE2" Residue "A GLU 477": "OE1" <-> "OE2" Residue "A GLU 522": "OE1" <-> "OE2" Residue "A GLU 525": "OE1" <-> "OE2" Residue "A GLU 562": "OE1" <-> "OE2" Residue "A GLU 595": "OE1" <-> "OE2" Residue "A GLU 605": "OE1" <-> "OE2" Residue "A GLU 631": "OE1" <-> "OE2" Residue "A GLU 811": "OE1" <-> "OE2" Residue "A GLU 813": "OE1" <-> "OE2" Residue "A GLU 879": "OE1" <-> "OE2" Residue "A GLU 937": "OE1" <-> "OE2" Residue "B GLU 53": "OE1" <-> "OE2" Residue "B GLU 64": "OE1" <-> "OE2" Residue "B GLU 236": "OE1" <-> "OE2" Residue "B GLU 287": "OE1" <-> "OE2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B GLU 336": "OE1" <-> "OE2" Residue "B GLU 358": "OE1" <-> "OE2" Residue "C ASP 34": "OD1" <-> "OD2" Residue "C GLU 302": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 8384 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4403 Classifications: {'peptide': 536} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 17, 'TRANS': 518} Chain breaks: 3 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 2956 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 368, 2956 Classifications: {'peptide': 368} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 351} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1004 Classifications: {'peptide': 126} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 113} Chain breaks: 1 Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 7 Unusual residues: {' CA': 2, ' ZN': 1, 'ACT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7743 SG CYS C 289 37.781 59.224 44.747 1.00 57.24 S ATOM 7769 SG CYS C 292 35.184 57.659 42.331 1.00 45.08 S ATOM 7952 SG CYS C 315 38.825 56.578 42.087 1.00 59.56 S ATOM 7627 SG CYS C 274 37.775 47.115 47.263 1.00 38.25 S ATOM 7651 SG CYS C 277 37.170 43.505 48.360 1.00 48.40 S ATOM 7835 SG CYS C 300 40.704 44.735 47.787 1.00 41.17 S Time building chain proxies: 4.96, per 1000 atoms: 0.59 Number of scatterers: 8384 At special positions: 0 Unit cell: (122.094, 92.34, 109.782, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 Ca 2 19.99 S 55 16.00 O 1548 8.00 N 1447 7.00 C 5329 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 3.29 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" ND1 HIS B 179 " pdb=" ZN C1101 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 318 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 292 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 315 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 289 " pdb=" ZN C1102 " pdb="ZN ZN C1102 " - pdb=" ND1 HIS C 297 " pdb="ZN ZN C1102 " - pdb=" SG CYS C 300 " pdb="ZN ZN C1102 " - pdb=" SG CYS C 277 " pdb="ZN ZN C1102 " - pdb=" SG CYS C 274 " Number of angles added : 6 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1950 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 41 helices and 5 sheets defined 53.2% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'A' and resid 305 through 318 Processing helix chain 'A' and resid 322 through 335 Processing helix chain 'A' and resid 341 through 348 Processing helix chain 'A' and resid 356 through 366 Processing helix chain 'A' and resid 418 through 423 Processing helix chain 'A' and resid 447 through 485 removed outlier: 3.726A pdb=" N GLN A 451 " --> pdb=" O PRO A 447 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU A 452 " --> pdb=" O TYR A 448 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 462 " --> pdb=" O GLU A 458 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG A 485 " --> pdb=" O LYS A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 493 removed outlier: 4.222A pdb=" N GLU A 492 " --> pdb=" O PRO A 488 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N LYS A 493 " --> pdb=" O GLU A 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 488 through 493' Processing helix chain 'A' and resid 507 through 529 removed outlier: 7.562A pdb=" N ASP A 518 " --> pdb=" O ARG A 514 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N LYS A 519 " --> pdb=" O ILE A 515 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) Proline residue: A 521 - end of helix Processing helix chain 'A' and resid 531 through 560 Proline residue: A 536 - end of helix Processing helix chain 'A' and resid 564 through 572 removed outlier: 5.035A pdb=" N LEU A 569 " --> pdb=" O GLU A 565 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N LYS A 570 " --> pdb=" O LYS A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 586 removed outlier: 4.095A pdb=" N GLN A 581 " --> pdb=" O VAL A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 609 removed outlier: 3.557A pdb=" N ILE A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL A 599 " --> pdb=" O GLU A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 643 removed outlier: 3.851A pdb=" N ARG A 643 " --> pdb=" O TYR A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 660 Processing helix chain 'A' and resid 662 through 666 Processing helix chain 'A' and resid 747 through 785 Processing helix chain 'A' and resid 789 through 791 No H-bonds generated for 'chain 'A' and resid 789 through 791' Processing helix chain 'A' and resid 809 through 828 removed outlier: 5.040A pdb=" N TYR A 816 " --> pdb=" O LEU A 812 " (cutoff:3.500A) Proline residue: A 817 - end of helix Processing helix chain 'A' and resid 833 through 851 removed outlier: 8.070A pdb=" N ILE A 846 " --> pdb=" O GLU A 842 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N HIS A 847 " --> pdb=" O MET A 843 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA A 848 " --> pdb=" O PHE A 844 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N TYR A 849 " --> pdb=" O THR A 845 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N VAL A 850 " --> pdb=" O ILE A 846 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N GLY A 851 " --> pdb=" O HIS A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 870 Processing helix chain 'A' and resid 872 through 887 removed outlier: 3.593A pdb=" N ARG A 887 " --> pdb=" O ASN A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 914 removed outlier: 3.853A pdb=" N CYS A 898 " --> pdb=" O SER A 895 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA A 901 " --> pdb=" O CYS A 898 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ALA A 902 " --> pdb=" O VAL A 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 22 No H-bonds generated for 'chain 'B' and resid 20 through 22' Processing helix chain 'B' and resid 33 through 45 Processing helix chain 'B' and resid 62 through 67 removed outlier: 3.893A pdb=" N LYS B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 79 Processing helix chain 'B' and resid 82 through 84 No H-bonds generated for 'chain 'B' and resid 82 through 84' Processing helix chain 'B' and resid 86 through 94 removed outlier: 4.014A pdb=" N SER B 89 " --> pdb=" O SER B 86 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LYS B 90 " --> pdb=" O GLU B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 126 removed outlier: 3.702A pdb=" N SER B 118 " --> pdb=" O SER B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 166 removed outlier: 4.076A pdb=" N LYS B 166 " --> pdb=" O LEU B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 187 Processing helix chain 'B' and resid 218 through 220 No H-bonds generated for 'chain 'B' and resid 218 through 220' Processing helix chain 'B' and resid 235 through 253 removed outlier: 3.618A pdb=" N LYS B 243 " --> pdb=" O GLY B 239 " (cutoff:3.500A) Proline residue: B 244 - end of helix Processing helix chain 'B' and resid 279 through 292 removed outlier: 4.069A pdb=" N CYS B 285 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N VAL B 286 " --> pdb=" O HIS B 282 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N PHE B 292 " --> pdb=" O VAL B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 320 Processing helix chain 'B' and resid 335 through 338 Processing helix chain 'B' and resid 357 through 373 removed outlier: 3.950A pdb=" N MET B 373 " --> pdb=" O GLU B 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 27 Processing helix chain 'C' and resid 320 through 325 Processing helix chain 'C' and resid 331 through 341 removed outlier: 4.070A pdb=" N PHE C 341 " --> pdb=" O VAL C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 359 Processing sheet with id= A, first strand: chain 'A' and resid 401 through 403 Processing sheet with id= B, first strand: chain 'A' and resid 620 through 624 removed outlier: 4.314A pdb=" N VAL A 739 " --> pdb=" O GLN A 927 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 13 through 15 removed outlier: 6.233A pdb=" N GLU B 53 " --> pdb=" O TYR B 14 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 132 through 135 removed outlier: 6.712A pdb=" N LEU B 296 " --> pdb=" O ALA B 133 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N ASN B 135 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N MET B 298 " --> pdb=" O ASN B 135 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 286 through 288 386 hydrogen bonds defined for protein. 1062 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: 2.13 Time building geometry restraints manager: 3.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2745 1.34 - 1.46: 1962 1.46 - 1.58: 3767 1.58 - 1.71: 0 1.71 - 1.83: 82 Bond restraints: 8556 Sorted by residual: bond pdb=" N THR C 33 " pdb=" CA THR C 33 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.25e-02 6.40e+03 8.40e+00 bond pdb=" N LYS C 32 " pdb=" CA LYS C 32 " ideal model delta sigma weight residual 1.457 1.493 -0.035 1.29e-02 6.01e+03 7.43e+00 bond pdb=" N CYS A 788 " pdb=" CA CYS A 788 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.33e-02 5.65e+03 6.33e+00 bond pdb=" C PRO C 30 " pdb=" N PRO C 31 " ideal model delta sigma weight residual 1.335 1.368 -0.033 1.30e-02 5.92e+03 6.29e+00 bond pdb=" N LEU A 787 " pdb=" CA LEU A 787 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.22e-02 6.72e+03 6.18e+00 ... (remaining 8551 not shown) Histogram of bond angle deviations from ideal: 100.24 - 107.00: 243 107.00 - 113.75: 4606 113.75 - 120.50: 3496 120.50 - 127.25: 3107 127.25 - 134.00: 93 Bond angle restraints: 11545 Sorted by residual: angle pdb=" O PRO C 30 " pdb=" C PRO C 30 " pdb=" N PRO C 31 " ideal model delta sigma weight residual 121.31 117.41 3.90 4.60e-01 4.73e+00 7.20e+01 angle pdb=" CA PRO C 30 " pdb=" C PRO C 30 " pdb=" N PRO C 31 " ideal model delta sigma weight residual 117.73 121.74 -4.01 9.00e-01 1.23e+00 1.99e+01 angle pdb=" C GLU A 789 " pdb=" CA GLU A 789 " pdb=" CB GLU A 789 " ideal model delta sigma weight residual 116.63 111.50 5.13 1.16e+00 7.43e-01 1.96e+01 angle pdb=" N CYS A 788 " pdb=" CA CYS A 788 " pdb=" C CYS A 788 " ideal model delta sigma weight residual 113.28 108.13 5.15 1.22e+00 6.72e-01 1.78e+01 angle pdb=" CA GLU A 562 " pdb=" CB GLU A 562 " pdb=" CG GLU A 562 " ideal model delta sigma weight residual 114.10 121.34 -7.24 2.00e+00 2.50e-01 1.31e+01 ... (remaining 11540 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 4418 17.81 - 35.63: 528 35.63 - 53.44: 184 53.44 - 71.26: 33 71.26 - 89.07: 12 Dihedral angle restraints: 5175 sinusoidal: 2151 harmonic: 3024 Sorted by residual: dihedral pdb=" CA THR B 305 " pdb=" C THR B 305 " pdb=" N ILE B 306 " pdb=" CA ILE B 306 " ideal model delta harmonic sigma weight residual -180.00 -157.69 -22.31 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA GLU A 562 " pdb=" C GLU A 562 " pdb=" N GLN A 563 " pdb=" CA GLN A 563 " ideal model delta harmonic sigma weight residual 180.00 159.50 20.50 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA TYR B 304 " pdb=" C TYR B 304 " pdb=" N THR B 305 " pdb=" CA THR B 305 " ideal model delta harmonic sigma weight residual 180.00 160.83 19.17 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 5172 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 787 0.034 - 0.067: 327 0.067 - 0.101: 81 0.101 - 0.135: 36 0.135 - 0.168: 2 Chirality restraints: 1233 Sorted by residual: chirality pdb=" CA LEU A 786 " pdb=" N LEU A 786 " pdb=" C LEU A 786 " pdb=" CB LEU A 786 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.09e-01 chirality pdb=" CA GLU A 562 " pdb=" N GLU A 562 " pdb=" C GLU A 562 " pdb=" CB GLU A 562 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.45e-01 chirality pdb=" CA VAL B 171 " pdb=" N VAL B 171 " pdb=" C VAL B 171 " pdb=" CB VAL B 171 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.12e-01 ... (remaining 1230 not shown) Planarity restraints: 1498 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 269 " -0.031 5.00e-02 4.00e+02 4.73e-02 3.59e+00 pdb=" N PRO C 270 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO C 270 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 270 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR B 39 " 0.008 2.00e-02 2.50e+03 1.65e-02 2.72e+00 pdb=" C THR B 39 " -0.029 2.00e-02 2.50e+03 pdb=" O THR B 39 " 0.011 2.00e-02 2.50e+03 pdb=" N HIS B 40 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 864 " 0.008 2.00e-02 2.50e+03 1.53e-02 2.34e+00 pdb=" C GLN A 864 " -0.026 2.00e-02 2.50e+03 pdb=" O GLN A 864 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU A 865 " 0.009 2.00e-02 2.50e+03 ... (remaining 1495 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.38: 25 2.38 - 3.01: 4710 3.01 - 3.64: 12425 3.64 - 4.27: 19176 4.27 - 4.90: 32011 Nonbonded interactions: 68347 Sorted by model distance: nonbonded pdb=" O ASN B 22 " pdb=" O HOH B 601 " model vdw 1.755 2.440 nonbonded pdb="ZN ZN B 501 " pdb=" O ACT B 504 " model vdw 1.878 2.230 nonbonded pdb=" OD2 ASP B 265 " pdb="ZN ZN B 501 " model vdw 1.918 2.230 nonbonded pdb=" OD1 ASP B 177 " pdb="ZN ZN B 501 " model vdw 1.947 2.230 nonbonded pdb=" O HOH A1204 " pdb=" O HOH A1205 " model vdw 1.993 2.440 ... (remaining 68342 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 0.400 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: 2.250 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 27.330 Find NCS groups from input model: 0.220 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: 0.000 Load rotamer database and sin/cos tables:11.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 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 : 0.004 0.064 8556 Z= 0.229 Angle : 0.614 10.634 11545 Z= 0.360 Chirality : 0.041 0.168 1233 Planarity : 0.004 0.047 1498 Dihedral : 17.771 89.069 3225 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.96 % Allowed : 24.59 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % 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: 0.64 (0.26), residues: 1016 helix: 1.17 (0.23), residues: 550 sheet: 0.78 (0.62), residues: 76 loop : -0.67 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 909 HIS 0.007 0.001 HIS A 867 PHE 0.012 0.001 PHE A 744 TYR 0.014 0.001 TYR B 304 ARG 0.004 0.000 ARG C 279 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 91 time to evaluate : 0.940 Fit side-chains REVERT: A 449 GLU cc_start: 0.7625 (mm-30) cc_final: 0.7423 (mm-30) REVERT: A 668 PHE cc_start: 0.4109 (OUTLIER) cc_final: 0.3499 (m-10) outliers start: 27 outliers final: 21 residues processed: 115 average time/residue: 1.2147 time to fit residues: 149.4990 Evaluate side-chains 113 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 91 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 668 PHE Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 349 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 40 optimal weight: 0.0770 chunk 79 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 48 optimal weight: 6.9990 chunk 58 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 648 GLN ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 HIS ** C 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.0482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8556 Z= 0.160 Angle : 0.488 6.679 11545 Z= 0.258 Chirality : 0.039 0.137 1233 Planarity : 0.004 0.041 1498 Dihedral : 6.149 45.286 1165 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 4.39 % Allowed : 22.94 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % 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: 0.98 (0.27), residues: 1016 helix: 1.48 (0.23), residues: 551 sheet: 0.95 (0.63), residues: 76 loop : -0.57 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 909 HIS 0.008 0.001 HIS A 867 PHE 0.010 0.001 PHE B 335 TYR 0.013 0.001 TYR B 304 ARG 0.003 0.000 ARG C 279 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 100 time to evaluate : 0.956 Fit side-chains REVERT: A 327 PHE cc_start: 0.7684 (t80) cc_final: 0.7336 (t80) REVERT: A 449 GLU cc_start: 0.7574 (mm-30) cc_final: 0.7293 (mm-30) REVERT: A 668 PHE cc_start: 0.4290 (OUTLIER) cc_final: 0.3642 (m-10) REVERT: A 842 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7682 (pt0) REVERT: A 865 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7745 (mt) REVERT: A 867 HIS cc_start: 0.7034 (t70) cc_final: 0.6751 (t70) REVERT: A 937 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7699 (pt0) REVERT: B 53 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7449 (mt-10) REVERT: C 302 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.6988 (mm-30) REVERT: C 347 GLN cc_start: 0.3233 (OUTLIER) cc_final: 0.3001 (pt0) outliers start: 40 outliers final: 18 residues processed: 128 average time/residue: 1.2079 time to fit residues: 164.7101 Evaluate side-chains 118 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 93 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 668 PHE Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 842 GLU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 347 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 0.9980 chunk 28 optimal weight: 0.0040 chunk 76 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 91 optimal weight: 9.9990 chunk 99 optimal weight: 9.9990 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 73 optimal weight: 0.0170 chunk 90 optimal weight: 4.9990 overall best weight: 0.8034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 ASN ** C 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.0683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8556 Z= 0.166 Angle : 0.482 6.707 11545 Z= 0.254 Chirality : 0.038 0.131 1233 Planarity : 0.003 0.037 1498 Dihedral : 5.438 46.702 1152 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 5.05 % Allowed : 23.16 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % 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: 1.07 (0.27), residues: 1016 helix: 1.56 (0.23), residues: 550 sheet: 1.04 (0.63), residues: 76 loop : -0.55 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 909 HIS 0.006 0.001 HIS A 867 PHE 0.010 0.001 PHE A 744 TYR 0.011 0.001 TYR B 304 ARG 0.002 0.000 ARG B 127 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 101 time to evaluate : 0.946 Fit side-chains REVERT: A 327 PHE cc_start: 0.7672 (t80) cc_final: 0.7384 (t80) REVERT: A 449 GLU cc_start: 0.7612 (mm-30) cc_final: 0.7341 (mm-30) REVERT: A 668 PHE cc_start: 0.4436 (OUTLIER) cc_final: 0.3663 (m-10) REVERT: A 842 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7714 (pt0) REVERT: A 865 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7809 (mt) REVERT: A 867 HIS cc_start: 0.7063 (t70) cc_final: 0.6784 (t70) REVERT: A 880 LEU cc_start: 0.7856 (tp) cc_final: 0.7152 (mt) REVERT: A 937 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7656 (pt0) REVERT: B 53 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7465 (mt-10) REVERT: B 94 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7245 (ttm170) REVERT: C 302 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.6979 (mm-30) outliers start: 46 outliers final: 20 residues processed: 134 average time/residue: 1.2318 time to fit residues: 175.8161 Evaluate side-chains 120 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 93 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 668 PHE Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 842 GLU Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 94 ARG Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 319 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 61 optimal weight: 0.6980 chunk 92 optimal weight: 0.0020 chunk 97 optimal weight: 10.0000 chunk 48 optimal weight: 0.6980 chunk 87 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 chunk 81 optimal weight: 0.2980 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.0883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8556 Z= 0.133 Angle : 0.464 6.158 11545 Z= 0.245 Chirality : 0.037 0.132 1233 Planarity : 0.003 0.034 1498 Dihedral : 5.256 48.919 1151 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 4.06 % Allowed : 24.04 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.27), residues: 1016 helix: 1.65 (0.23), residues: 550 sheet: 1.11 (0.63), residues: 76 loop : -0.52 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 909 HIS 0.006 0.001 HIS C 318 PHE 0.008 0.001 PHE B 335 TYR 0.011 0.001 TYR B 304 ARG 0.003 0.000 ARG B 127 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 101 time to evaluate : 0.875 Fit side-chains REVERT: A 327 PHE cc_start: 0.7595 (t80) cc_final: 0.7301 (t80) REVERT: A 449 GLU cc_start: 0.7534 (mm-30) cc_final: 0.7254 (mm-30) REVERT: A 450 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.6805 (mm-30) REVERT: A 668 PHE cc_start: 0.4334 (OUTLIER) cc_final: 0.3623 (m-10) REVERT: A 842 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7695 (pt0) REVERT: A 865 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7826 (mt) REVERT: A 880 LEU cc_start: 0.7778 (tp) cc_final: 0.7092 (mt) REVERT: A 937 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7612 (pt0) REVERT: B 53 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7422 (mt-10) REVERT: B 94 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.7274 (ttm170) REVERT: C 302 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.6977 (mm-30) outliers start: 37 outliers final: 14 residues processed: 128 average time/residue: 1.2404 time to fit residues: 169.1350 Evaluate side-chains 112 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 90 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 668 PHE Chi-restraints excluded: chain A residue 842 GLU Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 94 ARG Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 349 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 chunk 87 optimal weight: 0.4980 chunk 24 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 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 578 ASN ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN ** C 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.0940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8556 Z= 0.161 Angle : 0.478 6.893 11545 Z= 0.251 Chirality : 0.038 0.125 1233 Planarity : 0.003 0.033 1498 Dihedral : 5.305 50.003 1150 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 4.83 % Allowed : 23.82 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.27), residues: 1016 helix: 1.63 (0.23), residues: 550 sheet: 1.15 (0.63), residues: 76 loop : -0.48 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 313 HIS 0.008 0.001 HIS C 318 PHE 0.009 0.001 PHE A 744 TYR 0.012 0.001 TYR B 304 ARG 0.002 0.000 ARG A 396 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 97 time to evaluate : 1.110 Fit side-chains REVERT: A 450 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.6913 (mm-30) REVERT: A 668 PHE cc_start: 0.4338 (OUTLIER) cc_final: 0.3696 (m-10) REVERT: A 842 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7769 (pt0) REVERT: A 865 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7856 (mt) REVERT: A 937 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7598 (pt0) REVERT: B 53 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7416 (mt-10) REVERT: B 94 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7306 (ttm170) REVERT: B 322 ASP cc_start: 0.8348 (OUTLIER) cc_final: 0.8050 (t0) REVERT: C 302 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.7000 (mm-30) outliers start: 44 outliers final: 24 residues processed: 129 average time/residue: 1.1970 time to fit residues: 164.7087 Evaluate side-chains 121 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 88 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 628 GLN Chi-restraints excluded: chain A residue 668 PHE Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 842 GLU Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 94 ARG Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 349 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 chunk 81 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 8 optimal weight: 0.0770 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 94 optimal weight: 7.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8556 Z= 0.156 Angle : 0.480 8.393 11545 Z= 0.251 Chirality : 0.038 0.122 1233 Planarity : 0.003 0.033 1498 Dihedral : 5.320 49.888 1150 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 4.72 % Allowed : 24.04 % Favored : 71.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % 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: 1.21 (0.27), residues: 1016 helix: 1.65 (0.23), residues: 550 sheet: 1.20 (0.63), residues: 76 loop : -0.47 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 313 HIS 0.006 0.001 HIS C 318 PHE 0.008 0.001 PHE B 335 TYR 0.012 0.001 TYR B 304 ARG 0.003 0.000 ARG B 127 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 93 time to evaluate : 1.058 Fit side-chains REVERT: A 319 LYS cc_start: 0.7149 (mmmt) cc_final: 0.6679 (mttt) REVERT: A 327 PHE cc_start: 0.7596 (t80) cc_final: 0.7263 (t80) REVERT: A 450 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.6943 (mm-30) REVERT: A 842 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7696 (pt0) REVERT: A 865 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7858 (mt) REVERT: A 880 LEU cc_start: 0.7917 (tp) cc_final: 0.7647 (tt) REVERT: A 927 GLN cc_start: 0.6342 (mp10) cc_final: 0.5993 (mp10) REVERT: A 937 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7641 (pt0) REVERT: B 53 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7401 (mt-10) REVERT: B 94 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7294 (ttm170) REVERT: B 322 ASP cc_start: 0.8340 (OUTLIER) cc_final: 0.8042 (t0) REVERT: C 302 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.6967 (mm-30) outliers start: 43 outliers final: 20 residues processed: 123 average time/residue: 1.3777 time to fit residues: 180.8182 Evaluate side-chains 119 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 91 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain A residue 628 GLN Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 842 GLU Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 94 ARG Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 349 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 97 optimal weight: 0.0870 chunk 60 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 58 optimal weight: 0.3980 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 HIS ** C 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8556 Z= 0.152 Angle : 0.472 8.388 11545 Z= 0.247 Chirality : 0.038 0.126 1233 Planarity : 0.003 0.033 1498 Dihedral : 5.300 58.393 1147 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 5.05 % Allowed : 23.82 % Favored : 71.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.27), residues: 1016 helix: 1.67 (0.23), residues: 550 sheet: 1.24 (0.63), residues: 76 loop : -0.42 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 313 HIS 0.006 0.001 HIS C 318 PHE 0.009 0.001 PHE B 335 TYR 0.011 0.001 TYR B 304 ARG 0.003 0.000 ARG B 127 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 94 time to evaluate : 1.120 Fit side-chains REVERT: A 319 LYS cc_start: 0.7206 (mmmt) cc_final: 0.6705 (mttt) REVERT: A 450 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.6943 (mm-30) REVERT: A 668 PHE cc_start: 0.4396 (OUTLIER) cc_final: 0.3580 (m-10) REVERT: A 842 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7695 (pt0) REVERT: A 865 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7858 (mt) REVERT: A 880 LEU cc_start: 0.7889 (tp) cc_final: 0.7595 (tt) REVERT: A 927 GLN cc_start: 0.6367 (mp10) cc_final: 0.5893 (mp10) REVERT: A 937 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7629 (pt0) REVERT: B 53 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7394 (mt-10) REVERT: B 94 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7278 (ttm170) REVERT: B 322 ASP cc_start: 0.8355 (OUTLIER) cc_final: 0.8071 (t0) REVERT: C 302 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.6974 (mm-30) outliers start: 46 outliers final: 22 residues processed: 128 average time/residue: 1.2052 time to fit residues: 164.9016 Evaluate side-chains 121 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 90 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 628 GLN Chi-restraints excluded: chain A residue 668 PHE Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 842 GLU Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 94 ARG Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 349 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 66 optimal weight: 7.9990 chunk 48 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 931 GLN C 288 GLN ** C 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8556 Z= 0.259 Angle : 0.551 9.034 11545 Z= 0.285 Chirality : 0.040 0.121 1233 Planarity : 0.004 0.033 1498 Dihedral : 5.553 59.312 1147 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 4.94 % Allowed : 24.15 % Favored : 70.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % 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: 1.05 (0.27), residues: 1016 helix: 1.52 (0.23), residues: 549 sheet: 1.22 (0.64), residues: 76 loop : -0.56 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 313 HIS 0.008 0.001 HIS A 867 PHE 0.012 0.002 PHE A 744 TYR 0.014 0.002 TYR B 304 ARG 0.004 0.000 ARG A 396 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 94 time to evaluate : 0.977 Fit side-chains REVERT: A 319 LYS cc_start: 0.7197 (mmmt) cc_final: 0.6694 (mttt) REVERT: A 327 PHE cc_start: 0.7461 (t80) cc_final: 0.7181 (t80) REVERT: A 449 GLU cc_start: 0.7424 (mm-30) cc_final: 0.7139 (mm-30) REVERT: A 450 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7003 (mm-30) REVERT: A 865 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7903 (mt) REVERT: A 880 LEU cc_start: 0.7950 (tp) cc_final: 0.7249 (mt) REVERT: A 927 GLN cc_start: 0.6259 (mp10) cc_final: 0.5764 (mp10) REVERT: A 937 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7645 (pt0) REVERT: B 53 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7436 (mt-10) REVERT: B 94 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.7249 (ttm170) REVERT: B 322 ASP cc_start: 0.8373 (OUTLIER) cc_final: 0.8035 (t0) REVERT: C 302 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.6950 (mm-30) outliers start: 45 outliers final: 27 residues processed: 127 average time/residue: 1.2706 time to fit residues: 172.2278 Evaluate side-chains 125 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 91 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 628 GLN Chi-restraints excluded: chain A residue 668 PHE Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 915 MET Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 94 ARG Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 349 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 64.6819 > 50: distance: 2 - 22: 19.857 distance: 18 - 22: 17.920 distance: 22 - 23: 10.058 distance: 23 - 24: 12.541 distance: 23 - 26: 20.313 distance: 24 - 25: 18.702 distance: 24 - 31: 12.553 distance: 26 - 27: 15.253 distance: 27 - 28: 40.455 distance: 28 - 29: 32.959 distance: 29 - 30: 22.762 distance: 31 - 32: 16.500 distance: 32 - 33: 16.086 distance: 32 - 35: 28.500 distance: 33 - 34: 32.279 distance: 33 - 39: 14.775 distance: 35 - 36: 37.139 distance: 36 - 38: 36.107 distance: 39 - 40: 48.451 distance: 40 - 41: 9.008 distance: 40 - 43: 33.214 distance: 41 - 42: 37.454 distance: 41 - 47: 31.028 distance: 44 - 46: 35.968 distance: 47 - 48: 10.671 distance: 48 - 51: 36.107 distance: 51 - 52: 25.324 distance: 53 - 54: 53.603 distance: 54 - 55: 15.654 distance: 54 - 57: 40.878 distance: 55 - 56: 42.254 distance: 55 - 62: 14.772 distance: 57 - 58: 43.047 distance: 58 - 59: 10.069 distance: 59 - 60: 44.601 distance: 59 - 61: 17.651 distance: 62 - 63: 37.663 distance: 64 - 65: 40.621 distance: 66 - 67: 47.402 distance: 67 - 68: 8.084 distance: 67 - 70: 18.248 distance: 68 - 69: 18.680 distance: 68 - 71: 26.196 distance: 71 - 72: 9.091 distance: 72 - 73: 6.201 distance: 73 - 74: 25.419 distance: 73 - 82: 42.998 distance: 75 - 76: 6.541 distance: 76 - 77: 17.568 distance: 77 - 78: 17.846 distance: 78 - 79: 23.141 distance: 79 - 80: 12.597 distance: 79 - 81: 14.589 distance: 82 - 83: 14.170 distance: 83 - 84: 27.346 distance: 83 - 86: 32.386 distance: 84 - 85: 11.068 distance: 86 - 87: 12.541 distance: 87 - 88: 5.325 distance: 88 - 90: 13.675 distance: 91 - 92: 14.590 distance: 92 - 93: 17.127 distance: 92 - 95: 11.078 distance: 93 - 94: 13.072 distance: 93 - 99: 30.120 distance: 95 - 96: 19.059 distance: 96 - 97: 11.099 distance: 96 - 98: 21.690