Starting phenix.real_space_refine on Fri Feb 14 21:16:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6m5v_30094/02_2025/6m5v_30094.cif Found real_map, /net/cci-nas-00/data/ceres_data/6m5v_30094/02_2025/6m5v_30094.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6m5v_30094/02_2025/6m5v_30094.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6m5v_30094/02_2025/6m5v_30094.map" model { file = "/net/cci-nas-00/data/ceres_data/6m5v_30094/02_2025/6m5v_30094.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6m5v_30094/02_2025/6m5v_30094.cif" } resolution = 4.5 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= 0.001 sd= 0.015 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: 9 Type Number sf(0) Gaussians Zn 2 6.06 5 P 2 5.49 5 Mg 1 5.21 5 S 47 5.16 5 Be 1 3.05 5 C 6703 2.51 5 N 1893 2.21 5 O 1897 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 86 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 10549 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4482 Classifications: {'peptide': 585} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 29, 'TRANS': 555} Chain breaks: 7 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 84 Chain: "B" Number of atoms: 5208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 670, 5208 Classifications: {'peptide': 670} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 33, 'TRANS': 636} Chain breaks: 4 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 825 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5415 SG CYS B 121 31.477 46.241 53.912 1.00 47.42 S ATOM 10277 SG CYS C 101 30.191 46.342 57.304 1.00 59.52 S ATOM 6010 SG CYS B 197 52.449 54.153 49.925 1.00 43.06 S ATOM 6028 SG CYS B 200 54.145 55.532 52.620 1.00 41.30 S Time building chain proxies: 6.20, per 1000 atoms: 0.59 Number of scatterers: 10549 At special positions: 0 Unit cell: (108.16, 101.92, 120.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 2 29.99 S 47 16.00 P 2 15.00 Mg 1 11.99 F 3 9.00 O 1897 8.00 N 1893 7.00 C 6703 6.00 Be 1 4.00 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 - 3.00 Amino acid : True - 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: 2.48 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 801 " pdb="ZN ZN B 801 " - pdb=" SG CYS B 121 " pdb="ZN ZN B 801 " - pdb=" SG CYS C 101 " pdb=" ZN B 802 " pdb="ZN ZN B 802 " - pdb=" SG CYS B 200 " pdb="ZN ZN B 802 " - pdb=" SG CYS B 197 " 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2566 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 7 sheets defined 53.3% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 67 through 72 Processing helix chain 'A' and resid 73 through 81 removed outlier: 4.300A pdb=" N VAL A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 removed outlier: 3.539A pdb=" N PHE A 85 " --> pdb=" O ARG A 81 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N SER A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU A 88 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL A 89 " --> pdb=" O PHE A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 118 Processing helix chain 'A' and resid 129 through 149 removed outlier: 3.731A pdb=" N GLN A 133 " --> pdb=" O ASP A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 167 removed outlier: 3.741A pdb=" N ASP A 162 " --> pdb=" O HIS A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 170 No H-bonds generated for 'chain 'A' and resid 168 through 170' Processing helix chain 'A' and resid 203 through 221 removed outlier: 4.173A pdb=" N LEU A 209 " --> pdb=" O GLN A 205 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE A 215 " --> pdb=" O HIS A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 236 Processing helix chain 'A' and resid 242 through 250 removed outlier: 3.673A pdb=" N VAL A 246 " --> pdb=" O SER A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 removed outlier: 3.710A pdb=" N VAL A 269 " --> pdb=" O THR A 265 " (cutoff:3.500A) Proline residue: A 270 - end of helix Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 365 through 373 removed outlier: 4.180A pdb=" N ILE A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 489 Processing helix chain 'A' and resid 496 through 500 Processing helix chain 'A' and resid 549 through 569 Processing helix chain 'A' and resid 585 through 601 Processing helix chain 'A' and resid 639 through 653 Processing helix chain 'A' and resid 672 through 682 Processing helix chain 'A' and resid 706 through 719 Processing helix chain 'B' and resid 6 through 33 removed outlier: 3.613A pdb=" N VAL B 10 " --> pdb=" O SER B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 41 Processing helix chain 'B' and resid 43 through 58 Processing helix chain 'B' and resid 61 through 70 Processing helix chain 'B' and resid 74 through 101 Processing helix chain 'B' and resid 106 through 115 removed outlier: 3.598A pdb=" N PHE B 110 " --> pdb=" O ASP B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 156 removed outlier: 3.633A pdb=" N VAL B 146 " --> pdb=" O PHE B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 180 removed outlier: 3.818A pdb=" N PHE B 175 " --> pdb=" O ARG B 171 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLY B 178 " --> pdb=" O GLU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 191 removed outlier: 3.788A pdb=" N SER B 191 " --> pdb=" O PRO B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 205 removed outlier: 3.786A pdb=" N PHE B 201 " --> pdb=" O CYS B 197 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU B 202 " --> pdb=" O ALA B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 217 Processing helix chain 'B' and resid 237 through 243 removed outlier: 3.525A pdb=" N TYR B 242 " --> pdb=" O GLU B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 265 Processing helix chain 'B' and resid 307 through 312 removed outlier: 4.104A pdb=" N GLN B 312 " --> pdb=" O SER B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 355 Processing helix chain 'B' and resid 374 through 381 removed outlier: 3.764A pdb=" N ILE B 381 " --> pdb=" O ASP B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 400 removed outlier: 3.867A pdb=" N ALA B 398 " --> pdb=" O ALA B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 414 Processing helix chain 'B' and resid 414 through 429 removed outlier: 3.554A pdb=" N CYS B 418 " --> pdb=" O SER B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 510 removed outlier: 3.557A pdb=" N LEU B 502 " --> pdb=" O GLU B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 531 removed outlier: 3.542A pdb=" N MET B 529 " --> pdb=" O GLU B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 560 removed outlier: 3.741A pdb=" N GLY B 549 " --> pdb=" O ALA B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 587 removed outlier: 3.936A pdb=" N ALA B 578 " --> pdb=" O GLY B 574 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N PHE B 581 " --> pdb=" O ASP B 577 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N MET B 582 " --> pdb=" O ALA B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 594 No H-bonds generated for 'chain 'B' and resid 592 through 594' Processing helix chain 'B' and resid 595 through 608 removed outlier: 4.314A pdb=" N HIS B 601 " --> pdb=" O PRO B 597 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE B 604 " --> pdb=" O THR B 600 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU B 606 " --> pdb=" O ARG B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 633 removed outlier: 3.912A pdb=" N SER B 630 " --> pdb=" O ALA B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 646 removed outlier: 3.643A pdb=" N GLU B 642 " --> pdb=" O PRO B 638 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N GLU B 643 " --> pdb=" O HIS B 639 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU B 644 " --> pdb=" O LEU B 640 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA B 645 " --> pdb=" O LYS B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 675 through 700 removed outlier: 3.534A pdb=" N GLN B 679 " --> pdb=" O ILE B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 772 removed outlier: 3.700A pdb=" N LEU B 769 " --> pdb=" O LEU B 765 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 35 removed outlier: 3.632A pdb=" N LEU C 30 " --> pdb=" O THR C 26 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL C 35 " --> pdb=" O ASP C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 80 removed outlier: 3.627A pdb=" N LEU C 78 " --> pdb=" O ARG C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 128 removed outlier: 3.676A pdb=" N GLU C 105 " --> pdb=" O CYS C 101 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA C 116 " --> pdb=" O GLU C 112 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N HIS C 125 " --> pdb=" O PHE C 121 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 58 through 59 Processing sheet with id=AA2, first strand: chain 'A' and resid 381 through 386 removed outlier: 7.623A pdb=" N THR A 254 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N SER A 384 " --> pdb=" O THR A 254 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N PHE A 256 " --> pdb=" O SER A 384 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N THR A 386 " --> pdb=" O PHE A 256 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL A 258 " --> pdb=" O THR A 386 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL A 255 " --> pdb=" O ASN A 408 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 286 through 287 Processing sheet with id=AA4, first strand: chain 'A' and resid 314 through 316 removed outlier: 3.656A pdb=" N SER A 332 " --> pdb=" O PHE A 324 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 616 through 619 removed outlier: 6.119A pdb=" N VAL A 576 " --> pdb=" O LEU A 618 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEU A 504 " --> pdb=" O ARG A 577 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N ALA A 579 " --> pdb=" O LEU A 504 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL A 506 " --> pdb=" O ALA A 579 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ASP A 503 " --> pdb=" O ARG A 528 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ARG A 528 " --> pdb=" O ASP A 503 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N THR A 521 " --> pdb=" O HIS A 540 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N HIS A 540 " --> pdb=" O THR A 521 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N VAL A 523 " --> pdb=" O LEU A 538 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU A 538 " --> pdb=" O VAL A 523 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL A 525 " --> pdb=" O PHE A 536 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N TYR A 533 " --> pdb=" O MET A 657 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N SER A 659 " --> pdb=" O TYR A 533 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ILE A 535 " --> pdb=" O SER A 659 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLU A 661 " --> pdb=" O ILE A 535 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ALA A 537 " --> pdb=" O GLU A 661 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL A 663 " --> pdb=" O ALA A 537 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N GLU A 539 " --> pdb=" O VAL A 663 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 125 through 126 Processing sheet with id=AA7, first strand: chain 'B' and resid 566 through 568 removed outlier: 6.363A pdb=" N ILE B 567 " --> pdb=" O TYR B 757 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL B 738 " --> pdb=" O TYR B 728 " (cutoff:3.500A) 499 hydrogen bonds defined for protein. 1452 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.00 Time building geometry restraints manager: 2.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1691 1.30 - 1.43: 2872 1.43 - 1.56: 6132 1.56 - 1.68: 13 1.68 - 1.81: 68 Bond restraints: 10776 Sorted by residual: bond pdb=" F3 BEF A 802 " pdb="BE BEF A 802 " ideal model delta sigma weight residual 1.476 1.765 -0.289 2.00e-02 2.50e+03 2.09e+02 bond pdb=" F1 BEF A 802 " pdb="BE BEF A 802 " ideal model delta sigma weight residual 1.476 1.765 -0.289 2.00e-02 2.50e+03 2.08e+02 bond pdb=" F2 BEF A 802 " pdb="BE BEF A 802 " ideal model delta sigma weight residual 1.476 1.764 -0.288 2.00e-02 2.50e+03 2.08e+02 bond pdb=" C ALA A 482 " pdb=" O ALA A 482 " ideal model delta sigma weight residual 1.237 1.172 0.064 1.17e-02 7.31e+03 3.02e+01 bond pdb=" C4 ADP A 801 " pdb=" C5 ADP A 801 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.01e+01 ... (remaining 10771 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 14168 2.17 - 4.34: 411 4.34 - 6.50: 48 6.50 - 8.67: 12 8.67 - 10.84: 4 Bond angle restraints: 14643 Sorted by residual: angle pdb=" C CYS A 125 " pdb=" N ALA A 126 " pdb=" CA ALA A 126 " ideal model delta sigma weight residual 122.52 130.37 -7.85 1.16e+00 7.43e-01 4.58e+01 angle pdb=" N VAL A 477 " pdb=" CA VAL A 477 " pdb=" C VAL A 477 " ideal model delta sigma weight residual 110.36 115.76 -5.40 1.05e+00 9.07e-01 2.64e+01 angle pdb=" N CYS A 125 " pdb=" CA CYS A 125 " pdb=" C CYS A 125 " ideal model delta sigma weight residual 108.42 116.12 -7.70 1.54e+00 4.22e-01 2.50e+01 angle pdb=" N ARG B 59 " pdb=" CA ARG B 59 " pdb=" C ARG B 59 " ideal model delta sigma weight residual 114.56 108.42 6.14 1.27e+00 6.20e-01 2.34e+01 angle pdb=" N SER A 481 " pdb=" CA SER A 481 " pdb=" C SER A 481 " ideal model delta sigma weight residual 111.07 106.34 4.73 1.07e+00 8.73e-01 1.96e+01 ... (remaining 14638 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.48: 5923 23.48 - 46.95: 420 46.95 - 70.43: 62 70.43 - 93.91: 12 93.91 - 117.38: 2 Dihedral angle restraints: 6419 sinusoidal: 2471 harmonic: 3948 Sorted by residual: dihedral pdb=" O2A ADP A 801 " pdb=" O3A ADP A 801 " pdb=" PA ADP A 801 " pdb=" PB ADP A 801 " ideal model delta sinusoidal sigma weight residual -60.00 57.38 -117.38 1 2.00e+01 2.50e-03 3.50e+01 dihedral pdb=" CA CYS B 223 " pdb=" C CYS B 223 " pdb=" N ASN B 224 " pdb=" CA ASN B 224 " ideal model delta harmonic sigma weight residual 180.00 152.99 27.01 0 5.00e+00 4.00e-02 2.92e+01 dihedral pdb=" C5' ADP A 801 " pdb=" O5' ADP A 801 " pdb=" PA ADP A 801 " pdb=" O2A ADP A 801 " ideal model delta sinusoidal sigma weight residual -60.00 37.46 -97.45 1 2.00e+01 2.50e-03 2.71e+01 ... (remaining 6416 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1469 0.073 - 0.146: 184 0.146 - 0.219: 22 0.219 - 0.292: 5 0.292 - 0.365: 1 Chirality restraints: 1681 Sorted by residual: chirality pdb=" CA VAL A 558 " pdb=" N VAL A 558 " pdb=" C VAL A 558 " pdb=" CB VAL A 558 " both_signs ideal model delta sigma weight residual False 2.44 2.08 0.37 2.00e-01 2.50e+01 3.34e+00 chirality pdb=" CA HIS B 535 " pdb=" N HIS B 535 " pdb=" C HIS B 535 " pdb=" CB HIS B 535 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA VAL A 663 " pdb=" N VAL A 663 " pdb=" C VAL A 663 " pdb=" CB VAL A 663 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.73e+00 ... (remaining 1678 not shown) Planarity restraints: 1892 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR B 242 " -0.016 2.00e-02 2.50e+03 3.26e-02 1.06e+01 pdb=" C TYR B 242 " 0.056 2.00e-02 2.50e+03 pdb=" O TYR B 242 " -0.021 2.00e-02 2.50e+03 pdb=" N LEU B 243 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 534 " 0.013 2.00e-02 2.50e+03 2.56e-02 6.54e+00 pdb=" C VAL B 534 " -0.044 2.00e-02 2.50e+03 pdb=" O VAL B 534 " 0.016 2.00e-02 2.50e+03 pdb=" N HIS B 535 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 724 " 0.036 5.00e-02 4.00e+02 5.48e-02 4.81e+00 pdb=" N PRO A 725 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 725 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 725 " 0.030 5.00e-02 4.00e+02 ... (remaining 1889 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1375 2.75 - 3.29: 10606 3.29 - 3.82: 17403 3.82 - 4.36: 20209 4.36 - 4.90: 34871 Nonbonded interactions: 84464 Sorted by model distance: nonbonded pdb=" O CYS B 223 " pdb=" ND1 HIS B 225 " model vdw 2.209 3.120 nonbonded pdb=" O CYS C 101 " pdb=" N GLY C 104 " model vdw 2.225 3.120 nonbonded pdb=" NE2 HIS B 157 " pdb=" O ASN B 608 " model vdw 2.269 3.120 nonbonded pdb=" O SER B 713 " pdb=" OG SER B 713 " model vdw 2.279 3.040 nonbonded pdb=" O GLY A 654 " pdb=" NH1 ARG C 120 " model vdw 2.281 3.120 ... (remaining 84459 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 0.260 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: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 26.690 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5902 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 : 0.007 0.289 10776 Z= 0.426 Angle : 0.865 10.839 14643 Z= 0.538 Chirality : 0.051 0.365 1681 Planarity : 0.005 0.055 1892 Dihedral : 16.072 117.384 3853 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 18.28 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.95 % Favored : 90.90 % Rotamer: Outliers : 5.50 % Allowed : 16.77 % Favored : 77.73 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % 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: -3.04 (0.21), residues: 1329 helix: -1.01 (0.18), residues: 692 sheet: -1.77 (0.52), residues: 92 loop : -3.41 (0.23), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 308 HIS 0.009 0.001 HIS A 540 PHE 0.023 0.002 PHE A 634 TYR 0.019 0.002 TYR A 507 ARG 0.005 0.000 ARG A 528 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 272 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 PHE cc_start: 0.6916 (t80) cc_final: 0.6557 (t80) REVERT: A 84 LEU cc_start: 0.8467 (tp) cc_final: 0.8061 (tp) REVERT: A 93 LEU cc_start: 0.8718 (mt) cc_final: 0.8170 (tt) REVERT: A 203 LEU cc_start: 0.8736 (tp) cc_final: 0.8425 (tp) REVERT: A 210 MET cc_start: 0.8690 (mtm) cc_final: 0.8197 (ttm) REVERT: A 213 THR cc_start: 0.8188 (m) cc_final: 0.7815 (p) REVERT: A 241 PHE cc_start: 0.8945 (OUTLIER) cc_final: 0.8679 (m-80) REVERT: A 249 PHE cc_start: 0.7879 (m-10) cc_final: 0.7323 (m-10) REVERT: A 271 LEU cc_start: 0.7751 (tt) cc_final: 0.7409 (tt) REVERT: A 600 MET cc_start: 0.6732 (mmp) cc_final: 0.6011 (tpt) REVERT: B 49 LEU cc_start: 0.7507 (OUTLIER) cc_final: 0.6350 (mt) REVERT: B 143 LEU cc_start: 0.7896 (mt) cc_final: 0.7646 (mt) REVERT: B 156 CYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8210 (m) REVERT: B 601 HIS cc_start: 0.8142 (m-70) cc_final: 0.7790 (m170) REVERT: B 690 ILE cc_start: 0.7997 (mt) cc_final: 0.7684 (tp) REVERT: B 748 CYS cc_start: 0.4796 (OUTLIER) cc_final: 0.4148 (t) REVERT: B 766 TYR cc_start: 0.6760 (t80) cc_final: 0.6452 (t80) REVERT: C 42 ASP cc_start: 0.6139 (t0) cc_final: 0.5889 (t0) REVERT: C 63 ASP cc_start: 0.8344 (m-30) cc_final: 0.7710 (m-30) REVERT: C 77 SER cc_start: 0.8905 (m) cc_final: 0.8335 (p) REVERT: C 79 LEU cc_start: 0.8452 (mt) cc_final: 0.8160 (tp) outliers start: 60 outliers final: 11 residues processed: 319 average time/residue: 0.3178 time to fit residues: 131.1818 Evaluate side-chains 171 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 156 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 56 optimal weight: 8.9990 chunk 34 optimal weight: 9.9990 chunk 69 optimal weight: 9.9990 chunk 54 optimal weight: 20.0000 chunk 105 optimal weight: 8.9990 chunk 40 optimal weight: 40.0000 chunk 64 optimal weight: 20.0000 chunk 78 optimal weight: 6.9990 chunk 122 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 HIS A 102 HIS ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 145 GLN A 148 HIS ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 375 GLN A 377 ASN A 670 GLN A 726 HIS B 68 GLN ** B 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 GLN ** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 HIS B 210 GLN B 323 GLN B 491 GLN B 614 HIS ** B 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 GLN C 119 ASN C 126 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.083847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.068929 restraints weight = 58979.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.070589 restraints weight = 41884.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.071782 restraints weight = 31942.005| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10776 Z= 0.323 Angle : 0.798 9.150 14643 Z= 0.407 Chirality : 0.045 0.200 1681 Planarity : 0.006 0.071 1892 Dihedral : 6.845 132.477 1501 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 17.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 0.18 % Allowed : 5.13 % Favored : 94.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.73 (0.23), residues: 1329 helix: 0.02 (0.19), residues: 697 sheet: -2.00 (0.47), residues: 105 loop : -2.57 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP A 308 HIS 0.011 0.002 HIS B 617 PHE 0.027 0.003 PHE A 241 TYR 0.025 0.002 TYR B 123 ARG 0.009 0.001 ARG B 62 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 173 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 PHE cc_start: 0.8957 (p90) cc_final: 0.8626 (p90) REVERT: A 210 MET cc_start: 0.9190 (mtm) cc_final: 0.8527 (ttm) REVERT: A 213 THR cc_start: 0.8842 (m) cc_final: 0.8301 (p) REVERT: A 216 LEU cc_start: 0.8885 (mt) cc_final: 0.8508 (pp) REVERT: A 249 PHE cc_start: 0.8952 (m-10) cc_final: 0.8273 (m-10) REVERT: A 299 GLU cc_start: 0.8816 (tp30) cc_final: 0.8500 (tp30) REVERT: A 335 VAL cc_start: 0.9417 (m) cc_final: 0.8999 (p) REVERT: A 600 MET cc_start: 0.8757 (mmp) cc_final: 0.8104 (tpt) REVERT: B 28 GLN cc_start: 0.9310 (mm-40) cc_final: 0.8862 (mm-40) REVERT: B 232 VAL cc_start: 0.8975 (p) cc_final: 0.8511 (p) REVERT: B 326 MET cc_start: 0.7011 (tpp) cc_final: 0.6792 (tpt) REVERT: B 375 MET cc_start: 0.6011 (mmm) cc_final: 0.5660 (mmm) REVERT: B 419 ASP cc_start: 0.8551 (p0) cc_final: 0.8089 (p0) REVERT: B 704 GLU cc_start: 0.9246 (pm20) cc_final: 0.8798 (pm20) REVERT: C 63 ASP cc_start: 0.8425 (m-30) cc_final: 0.7892 (m-30) outliers start: 2 outliers final: 2 residues processed: 175 average time/residue: 0.2891 time to fit residues: 67.8288 Evaluate side-chains 116 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 114 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 116 optimal weight: 1.9990 chunk 73 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 47 optimal weight: 30.0000 chunk 83 optimal weight: 7.9990 chunk 134 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 chunk 75 optimal weight: 1.9990 chunk 92 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 ASN ** B 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 HIS B 342 GLN B 491 GLN ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 ASN C 119 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.082519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.067765 restraints weight = 59723.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.069431 restraints weight = 41836.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.070605 restraints weight = 31582.315| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.4837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10776 Z= 0.242 Angle : 0.720 9.443 14643 Z= 0.359 Chirality : 0.043 0.143 1681 Planarity : 0.006 0.048 1892 Dihedral : 6.557 139.524 1501 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.24), residues: 1329 helix: 0.49 (0.20), residues: 701 sheet: -1.64 (0.49), residues: 99 loop : -2.39 (0.28), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 308 HIS 0.008 0.001 HIS B 617 PHE 0.021 0.002 PHE A 633 TYR 0.017 0.002 TYR B 123 ARG 0.009 0.001 ARG A 121 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8635 (mmtt) cc_final: 0.8326 (mmmt) REVERT: A 203 LEU cc_start: 0.8937 (tp) cc_final: 0.8507 (tt) REVERT: A 210 MET cc_start: 0.9070 (mtm) cc_final: 0.8567 (mtp) REVERT: A 299 GLU cc_start: 0.8884 (tp30) cc_final: 0.8542 (tp30) REVERT: A 324 PHE cc_start: 0.6372 (t80) cc_final: 0.6086 (t80) REVERT: A 335 VAL cc_start: 0.9452 (m) cc_final: 0.8997 (p) REVERT: A 600 MET cc_start: 0.8733 (mmp) cc_final: 0.8055 (tpt) REVERT: B 232 VAL cc_start: 0.8901 (p) cc_final: 0.8474 (p) REVERT: B 419 ASP cc_start: 0.8542 (p0) cc_final: 0.8106 (p0) REVERT: B 605 GLU cc_start: 0.9178 (mt-10) cc_final: 0.8529 (mt-10) REVERT: B 704 GLU cc_start: 0.9339 (pm20) cc_final: 0.8880 (pm20) REVERT: B 737 LEU cc_start: 0.8016 (mt) cc_final: 0.7746 (mt) REVERT: C 50 MET cc_start: 0.8071 (ttm) cc_final: 0.7088 (mmm) REVERT: C 63 ASP cc_start: 0.7879 (m-30) cc_final: 0.7188 (m-30) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.2611 time to fit residues: 55.7454 Evaluate side-chains 107 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 100 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 93 optimal weight: 20.0000 chunk 38 optimal weight: 20.0000 chunk 127 optimal weight: 0.4980 chunk 75 optimal weight: 6.9990 chunk 32 optimal weight: 20.0000 chunk 2 optimal weight: 7.9990 chunk 118 optimal weight: 20.0000 chunk 23 optimal weight: 7.9990 chunk 68 optimal weight: 30.0000 overall best weight: 5.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 211 HIS A 262 HIS ** B 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 491 GLN ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 ASN C 119 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.081607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.067741 restraints weight = 64894.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.069248 restraints weight = 46188.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.070336 restraints weight = 35268.422| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.5615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10776 Z= 0.290 Angle : 0.731 8.625 14643 Z= 0.372 Chirality : 0.043 0.206 1681 Planarity : 0.005 0.052 1892 Dihedral : 6.532 136.617 1501 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 19.38 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.73 % Favored : 91.20 % Rotamer: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.99 (0.24), residues: 1329 helix: 0.64 (0.20), residues: 691 sheet: -1.65 (0.52), residues: 88 loop : -2.22 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP A 308 HIS 0.008 0.001 HIS B 124 PHE 0.021 0.002 PHE A 279 TYR 0.014 0.002 TYR B 721 ARG 0.008 0.001 ARG B 60 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.9183 (mtm) cc_final: 0.8827 (mtt) REVERT: A 299 GLU cc_start: 0.8965 (tp30) cc_final: 0.8610 (tp30) REVERT: A 324 PHE cc_start: 0.6415 (t80) cc_final: 0.6089 (t80) REVERT: A 352 LEU cc_start: 0.8922 (mt) cc_final: 0.8680 (mt) REVERT: A 397 TYR cc_start: 0.7505 (m-80) cc_final: 0.7041 (m-80) REVERT: A 600 MET cc_start: 0.8884 (mmp) cc_final: 0.8139 (tpt) REVERT: B 155 TYR cc_start: 0.8161 (t80) cc_final: 0.7781 (t80) REVERT: B 232 VAL cc_start: 0.8578 (p) cc_final: 0.8313 (p) REVERT: B 326 MET cc_start: 0.6835 (tpt) cc_final: 0.6575 (tpt) REVERT: B 419 ASP cc_start: 0.8494 (p0) cc_final: 0.8006 (p0) REVERT: B 605 GLU cc_start: 0.9323 (mt-10) cc_final: 0.8645 (mt-10) REVERT: B 704 GLU cc_start: 0.9403 (pm20) cc_final: 0.8997 (pm20) REVERT: B 737 LEU cc_start: 0.7856 (mt) cc_final: 0.7520 (mt) REVERT: C 50 MET cc_start: 0.8098 (ttm) cc_final: 0.7003 (mmm) REVERT: C 63 ASP cc_start: 0.8068 (m-30) cc_final: 0.7472 (m-30) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.2599 time to fit residues: 50.1209 Evaluate side-chains 104 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 4 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 131 optimal weight: 9.9990 chunk 54 optimal weight: 5.9990 chunk 34 optimal weight: 20.0000 chunk 121 optimal weight: 20.0000 chunk 55 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 101 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 491 GLN ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 617 HIS B 771 HIS C 67 ASN C 119 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.078878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.064605 restraints weight = 59062.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.066165 restraints weight = 41793.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.067246 restraints weight = 31685.228| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.6169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10776 Z= 0.264 Angle : 0.722 10.123 14643 Z= 0.366 Chirality : 0.043 0.179 1681 Planarity : 0.005 0.051 1892 Dihedral : 6.549 135.706 1501 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 19.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.10 % Favored : 90.90 % Rotamer: Outliers : 0.09 % Allowed : 3.76 % Favored : 96.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.85 (0.24), residues: 1329 helix: 0.76 (0.20), residues: 695 sheet: -1.58 (0.53), residues: 86 loop : -2.17 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 308 HIS 0.021 0.002 HIS B 617 PHE 0.029 0.002 PHE A 241 TYR 0.017 0.002 TYR B 728 ARG 0.009 0.001 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 135 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8135 (mmtt) cc_final: 0.7741 (mmmt) REVERT: A 201 LEU cc_start: 0.9152 (mt) cc_final: 0.8635 (mt) REVERT: A 202 GLU cc_start: 0.8425 (tp30) cc_final: 0.8026 (tm-30) REVERT: A 203 LEU cc_start: 0.8925 (tt) cc_final: 0.8581 (tt) REVERT: A 204 PHE cc_start: 0.9207 (p90) cc_final: 0.8813 (p90) REVERT: A 205 GLN cc_start: 0.9496 (mm-40) cc_final: 0.9178 (mm110) REVERT: A 210 MET cc_start: 0.9193 (mtm) cc_final: 0.8591 (ttm) REVERT: A 226 GLU cc_start: 0.9279 (pm20) cc_final: 0.9047 (pp20) REVERT: A 299 GLU cc_start: 0.8810 (tp30) cc_final: 0.8418 (tp30) REVERT: A 324 PHE cc_start: 0.6556 (t80) cc_final: 0.6139 (t80) REVERT: A 352 LEU cc_start: 0.8746 (mt) cc_final: 0.8504 (mt) REVERT: A 397 TYR cc_start: 0.8019 (m-80) cc_final: 0.7170 (m-80) REVERT: A 500 MET cc_start: 0.3846 (mpp) cc_final: 0.3478 (mpp) REVERT: A 600 MET cc_start: 0.8295 (mmp) cc_final: 0.7564 (tpt) REVERT: B 155 TYR cc_start: 0.8313 (t80) cc_final: 0.8084 (t80) REVERT: B 232 VAL cc_start: 0.8687 (p) cc_final: 0.8388 (p) REVERT: B 326 MET cc_start: 0.7227 (tpt) cc_final: 0.6914 (tpt) REVERT: B 390 ASP cc_start: 0.9636 (t0) cc_final: 0.9185 (t0) REVERT: B 419 ASP cc_start: 0.8686 (p0) cc_final: 0.8245 (p0) REVERT: B 605 GLU cc_start: 0.9434 (mt-10) cc_final: 0.8737 (mt-10) REVERT: B 704 GLU cc_start: 0.9523 (pm20) cc_final: 0.8958 (pm20) REVERT: B 737 LEU cc_start: 0.7635 (mt) cc_final: 0.7285 (mt) REVERT: C 50 MET cc_start: 0.8164 (ttm) cc_final: 0.7136 (mmm) REVERT: C 63 ASP cc_start: 0.7977 (m-30) cc_final: 0.7375 (m-30) outliers start: 1 outliers final: 1 residues processed: 136 average time/residue: 0.2356 time to fit residues: 45.3700 Evaluate side-chains 107 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 106 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-5592/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-5592/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-5592/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-5592/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-5592/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-5592/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-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-5592/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-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.3864 > 50: distance: 10 - 33: 10.251 distance: 17 - 40: 19.164 distance: 25 - 50: 22.009 distance: 29 - 33: 10.884 distance: 30 - 61: 12.309 distance: 33 - 34: 10.318 distance: 34 - 35: 9.413 distance: 34 - 37: 7.329 distance: 35 - 36: 5.089 distance: 35 - 40: 3.918 distance: 36 - 68: 21.768 distance: 37 - 38: 18.880 distance: 37 - 39: 19.072 distance: 40 - 41: 7.094 distance: 41 - 42: 9.787 distance: 41 - 44: 3.872 distance: 42 - 43: 32.040 distance: 42 - 50: 4.993 distance: 44 - 45: 11.054 distance: 45 - 46: 11.172 distance: 45 - 47: 20.430 distance: 46 - 48: 10.918 distance: 47 - 49: 14.981 distance: 48 - 49: 15.966 distance: 51 - 52: 6.849 distance: 51 - 54: 6.979 distance: 52 - 53: 22.189 distance: 52 - 61: 17.087 distance: 53 - 87: 29.340 distance: 54 - 55: 11.303 distance: 55 - 56: 9.315 distance: 55 - 57: 7.465 distance: 56 - 58: 5.251 distance: 57 - 59: 3.042 distance: 58 - 60: 7.268 distance: 59 - 60: 8.911 distance: 61 - 62: 8.572 distance: 62 - 63: 13.972 distance: 62 - 65: 8.231 distance: 63 - 64: 14.506 distance: 63 - 68: 7.790 distance: 64 - 98: 4.067 distance: 65 - 66: 32.018 distance: 65 - 67: 10.054 distance: 68 - 69: 3.923 distance: 69 - 70: 7.450 distance: 69 - 72: 13.301 distance: 70 - 71: 9.905 distance: 70 - 79: 18.325 distance: 71 - 103: 28.305 distance: 72 - 73: 5.850 distance: 73 - 74: 13.156 distance: 74 - 75: 21.838 distance: 75 - 76: 11.382 distance: 76 - 77: 17.106 distance: 79 - 80: 17.786 distance: 80 - 81: 8.858 distance: 80 - 83: 11.136 distance: 81 - 82: 7.123 distance: 81 - 87: 8.108 distance: 82 - 112: 26.696 distance: 83 - 84: 6.950 distance: 84 - 85: 8.950 distance: 84 - 86: 6.156 distance: 87 - 88: 5.900 distance: 88 - 89: 9.304 distance: 88 - 91: 5.747 distance: 89 - 90: 26.467 distance: 89 - 98: 4.415 distance: 90 - 120: 22.393 distance: 91 - 92: 4.825 distance: 92 - 93: 5.060 distance: 92 - 94: 9.421 distance: 93 - 95: 5.876 distance: 94 - 96: 10.891 distance: 95 - 97: 8.055 distance: 96 - 97: 9.072 distance: 98 - 99: 43.917 distance: 99 - 100: 7.888 distance: 99 - 102: 4.973 distance: 100 - 101: 31.581 distance: 100 - 103: 35.323 distance: 103 - 104: 30.475 distance: 104 - 105: 19.976 distance: 104 - 107: 17.012 distance: 105 - 106: 18.147 distance: 105 - 112: 16.837 distance: 107 - 108: 15.943 distance: 108 - 109: 23.786 distance: 109 - 110: 19.513 distance: 109 - 111: 22.493 distance: 112 - 113: 7.162 distance: 113 - 114: 9.660 distance: 113 - 116: 9.911 distance: 114 - 115: 16.543 distance: 114 - 120: 13.726 distance: 116 - 117: 23.046 distance: 117 - 118: 17.987 distance: 117 - 119: 14.540