Starting phenix.real_space_refine on Mon May 19 21:07:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b3z_44161/05_2025/9b3z_44161.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b3z_44161/05_2025/9b3z_44161.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b3z_44161/05_2025/9b3z_44161.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b3z_44161/05_2025/9b3z_44161.map" model { file = "/net/cci-nas-00/data/ceres_data/9b3z_44161/05_2025/9b3z_44161.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b3z_44161/05_2025/9b3z_44161.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.052 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 P 4 5.49 5 S 116 5.16 5 B 4 2.79 5 C 12592 2.51 5 N 3204 2.21 5 O 3260 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 19180 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4724 Classifications: {'peptide': 594} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 576} Chain breaks: 4 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 4, 'GLU:plan': 10, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 94 Chain: "B" Number of atoms: 4724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4724 Classifications: {'peptide': 594} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 576} Chain breaks: 4 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 4, 'GLU:plan': 10, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 94 Chain: "C" Number of atoms: 4724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4724 Classifications: {'peptide': 594} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 576} Chain breaks: 4 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 4, 'GLU:plan': 10, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 94 Chain: "D" Number of atoms: 4724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4724 Classifications: {'peptide': 594} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 576} Chain breaks: 4 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 4, 'GLU:plan': 10, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 94 Chain: "A" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 71 Unusual residues: {'FZ4': 1, 'PEX': 1, 'RTO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 71 Unusual residues: {'FZ4': 1, 'PEX': 1, 'RTO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 71 Unusual residues: {'FZ4': 1, 'PEX': 1, 'RTO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 71 Unusual residues: {'FZ4': 1, 'PEX': 1, 'RTO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 10.69, per 1000 atoms: 0.56 Number of scatterers: 19180 At special positions: 0 Unit cell: (131.97, 131.97, 111.22, 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) S 116 16.00 P 4 15.00 O 3260 8.00 N 3204 7.00 C 12592 6.00 B 4 5.00 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: 4.78 Conformation dependent library (CDL) restraints added in 2.4 seconds 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4496 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 4 sheets defined 66.8% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'A' and resid 76 through 87 Processing helix chain 'A' and resid 88 through 91 Processing helix chain 'A' and resid 92 through 103 removed outlier: 4.490A pdb=" N LEU A 96 " --> pdb=" O LEU A 92 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLU A 97 " --> pdb=" O THR A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 112 Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.527A pdb=" N LEU A 126 " --> pdb=" O MET A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 147 removed outlier: 3.504A pdb=" N ASP A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 174 Processing helix chain 'A' and resid 176 through 186 Processing helix chain 'A' and resid 212 through 220 Processing helix chain 'A' and resid 222 through 232 removed outlier: 3.548A pdb=" N TYR A 228 " --> pdb=" O ASP A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 256 Processing helix chain 'A' and resid 262 through 282 removed outlier: 3.673A pdb=" N LEU A 266 " --> pdb=" O GLU A 262 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG A 280 " --> pdb=" O GLN A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 290 removed outlier: 3.667A pdb=" N ILE A 290 " --> pdb=" O LEU A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 306 Processing helix chain 'A' and resid 307 through 316 removed outlier: 3.663A pdb=" N HIS A 313 " --> pdb=" O GLU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 327 removed outlier: 4.237A pdb=" N TYR A 323 " --> pdb=" O SER A 320 " (cutoff:3.500A) Proline residue: A 325 - end of helix Processing helix chain 'A' and resid 355 through 362 Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.656A pdb=" N VAL A 373 " --> pdb=" O ARG A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 413 removed outlier: 4.965A pdb=" N SER A 391 " --> pdb=" O ASP A 387 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ARG A 392 " --> pdb=" O ARG A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 459 Processing helix chain 'A' and resid 470 through 492 Processing helix chain 'A' and resid 496 through 511 removed outlier: 3.628A pdb=" N LEU A 500 " --> pdb=" O TRP A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 518 removed outlier: 3.835A pdb=" N ARG A 517 " --> pdb=" O TYR A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 526 removed outlier: 3.608A pdb=" N ILE A 524 " --> pdb=" O GLN A 520 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N TYR A 525 " --> pdb=" O HIS A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 559 removed outlier: 3.616A pdb=" N LEU A 538 " --> pdb=" O LEU A 534 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG A 539 " --> pdb=" O ARG A 535 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL A 543 " --> pdb=" O ARG A 539 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE A 547 " --> pdb=" O VAL A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 605 removed outlier: 3.913A pdb=" N PHE A 603 " --> pdb=" O GLU A 599 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N THR A 604 " --> pdb=" O LEU A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 650 removed outlier: 3.998A pdb=" N GLU A 647 " --> pdb=" O ALA A 643 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N THR A 648 " --> pdb=" O LEU A 644 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL A 649 " --> pdb=" O MET A 645 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASN A 650 " --> pdb=" O SER A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 673 removed outlier: 4.001A pdb=" N TRP A 657 " --> pdb=" O ALA A 653 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASN A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 719 Processing helix chain 'B' and resid 76 through 87 Processing helix chain 'B' and resid 88 through 91 Processing helix chain 'B' and resid 92 through 103 removed outlier: 4.490A pdb=" N LEU B 96 " --> pdb=" O LEU B 92 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N GLU B 97 " --> pdb=" O THR B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 112 Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.527A pdb=" N LEU B 126 " --> pdb=" O MET B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 147 removed outlier: 3.504A pdb=" N ASP B 143 " --> pdb=" O LEU B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 174 Processing helix chain 'B' and resid 176 through 186 Processing helix chain 'B' and resid 212 through 220 Processing helix chain 'B' and resid 222 through 232 removed outlier: 3.548A pdb=" N TYR B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 256 Processing helix chain 'B' and resid 262 through 282 removed outlier: 3.673A pdb=" N LEU B 266 " --> pdb=" O GLU B 262 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG B 280 " --> pdb=" O GLN B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 290 removed outlier: 3.667A pdb=" N ILE B 290 " --> pdb=" O LEU B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 306 Processing helix chain 'B' and resid 307 through 316 removed outlier: 3.662A pdb=" N HIS B 313 " --> pdb=" O GLU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 327 removed outlier: 4.237A pdb=" N TYR B 323 " --> pdb=" O SER B 320 " (cutoff:3.500A) Proline residue: B 325 - end of helix Processing helix chain 'B' and resid 355 through 362 Processing helix chain 'B' and resid 368 through 373 removed outlier: 3.656A pdb=" N VAL B 373 " --> pdb=" O ARG B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 413 removed outlier: 4.965A pdb=" N SER B 391 " --> pdb=" O ASP B 387 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ARG B 392 " --> pdb=" O ARG B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 459 Processing helix chain 'B' and resid 470 through 492 Processing helix chain 'B' and resid 496 through 511 removed outlier: 3.629A pdb=" N LEU B 500 " --> pdb=" O TRP B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 518 removed outlier: 3.836A pdb=" N ARG B 517 " --> pdb=" O TYR B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 526 removed outlier: 3.608A pdb=" N ILE B 524 " --> pdb=" O GLN B 520 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N TYR B 525 " --> pdb=" O HIS B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 559 removed outlier: 3.616A pdb=" N LEU B 538 " --> pdb=" O LEU B 534 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG B 539 " --> pdb=" O ARG B 535 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL B 543 " --> pdb=" O ARG B 539 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE B 547 " --> pdb=" O VAL B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 605 removed outlier: 3.913A pdb=" N PHE B 603 " --> pdb=" O GLU B 599 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N THR B 604 " --> pdb=" O LEU B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 650 removed outlier: 3.999A pdb=" N GLU B 647 " --> pdb=" O ALA B 643 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N THR B 648 " --> pdb=" O LEU B 644 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL B 649 " --> pdb=" O MET B 645 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASN B 650 " --> pdb=" O SER B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 673 removed outlier: 4.001A pdb=" N TRP B 657 " --> pdb=" O ALA B 653 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASN B 673 " --> pdb=" O LEU B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 719 Processing helix chain 'C' and resid 76 through 87 Processing helix chain 'C' and resid 88 through 91 Processing helix chain 'C' and resid 92 through 103 removed outlier: 4.489A pdb=" N LEU C 96 " --> pdb=" O LEU C 92 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLU C 97 " --> pdb=" O THR C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 112 Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.526A pdb=" N LEU C 126 " --> pdb=" O MET C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 147 removed outlier: 3.504A pdb=" N ASP C 143 " --> pdb=" O LEU C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 174 Processing helix chain 'C' and resid 176 through 186 Processing helix chain 'C' and resid 212 through 220 Processing helix chain 'C' and resid 222 through 232 removed outlier: 3.548A pdb=" N TYR C 228 " --> pdb=" O ASP C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 256 Processing helix chain 'C' and resid 262 through 282 removed outlier: 3.672A pdb=" N LEU C 266 " --> pdb=" O GLU C 262 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG C 280 " --> pdb=" O GLN C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 290 removed outlier: 3.667A pdb=" N ILE C 290 " --> pdb=" O LEU C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 306 Processing helix chain 'C' and resid 307 through 316 removed outlier: 3.663A pdb=" N HIS C 313 " --> pdb=" O GLU C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 327 removed outlier: 4.237A pdb=" N TYR C 323 " --> pdb=" O SER C 320 " (cutoff:3.500A) Proline residue: C 325 - end of helix Processing helix chain 'C' and resid 355 through 362 Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.656A pdb=" N VAL C 373 " --> pdb=" O ARG C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 413 removed outlier: 4.964A pdb=" N SER C 391 " --> pdb=" O ASP C 387 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ARG C 392 " --> pdb=" O ARG C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 459 Processing helix chain 'C' and resid 470 through 492 Processing helix chain 'C' and resid 496 through 511 removed outlier: 3.629A pdb=" N LEU C 500 " --> pdb=" O TRP C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 518 removed outlier: 3.836A pdb=" N ARG C 517 " --> pdb=" O TYR C 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 526 removed outlier: 3.608A pdb=" N ILE C 524 " --> pdb=" O GLN C 520 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N TYR C 525 " --> pdb=" O HIS C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 559 removed outlier: 3.617A pdb=" N LEU C 538 " --> pdb=" O LEU C 534 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG C 539 " --> pdb=" O ARG C 535 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL C 543 " --> pdb=" O ARG C 539 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE C 547 " --> pdb=" O VAL C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 605 removed outlier: 3.913A pdb=" N PHE C 603 " --> pdb=" O GLU C 599 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N THR C 604 " --> pdb=" O LEU C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 650 removed outlier: 3.998A pdb=" N GLU C 647 " --> pdb=" O ALA C 643 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N THR C 648 " --> pdb=" O LEU C 644 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL C 649 " --> pdb=" O MET C 645 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASN C 650 " --> pdb=" O SER C 646 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 673 removed outlier: 4.001A pdb=" N TRP C 657 " --> pdb=" O ALA C 653 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASN C 673 " --> pdb=" O LEU C 669 " (cutoff:3.500A) Processing helix chain 'C' and resid 711 through 719 Processing helix chain 'D' and resid 76 through 87 Processing helix chain 'D' and resid 88 through 91 Processing helix chain 'D' and resid 92 through 103 removed outlier: 4.489A pdb=" N LEU D 96 " --> pdb=" O LEU D 92 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLU D 97 " --> pdb=" O THR D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 112 Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.526A pdb=" N LEU D 126 " --> pdb=" O MET D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 147 removed outlier: 3.504A pdb=" N ASP D 143 " --> pdb=" O LEU D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 174 Processing helix chain 'D' and resid 176 through 186 Processing helix chain 'D' and resid 212 through 220 Processing helix chain 'D' and resid 222 through 232 removed outlier: 3.548A pdb=" N TYR D 228 " --> pdb=" O ASP D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 256 Processing helix chain 'D' and resid 262 through 282 removed outlier: 3.673A pdb=" N LEU D 266 " --> pdb=" O GLU D 262 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG D 280 " --> pdb=" O GLN D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 290 removed outlier: 3.667A pdb=" N ILE D 290 " --> pdb=" O LEU D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 306 Processing helix chain 'D' and resid 307 through 316 removed outlier: 3.662A pdb=" N HIS D 313 " --> pdb=" O GLU D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 327 removed outlier: 4.237A pdb=" N TYR D 323 " --> pdb=" O SER D 320 " (cutoff:3.500A) Proline residue: D 325 - end of helix Processing helix chain 'D' and resid 355 through 362 Processing helix chain 'D' and resid 368 through 373 removed outlier: 3.656A pdb=" N VAL D 373 " --> pdb=" O ARG D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 413 removed outlier: 4.965A pdb=" N SER D 391 " --> pdb=" O ASP D 387 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ARG D 392 " --> pdb=" O ARG D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 459 Processing helix chain 'D' and resid 470 through 492 Processing helix chain 'D' and resid 496 through 511 removed outlier: 3.629A pdb=" N LEU D 500 " --> pdb=" O TRP D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 518 removed outlier: 3.836A pdb=" N ARG D 517 " --> pdb=" O TYR D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 526 removed outlier: 3.608A pdb=" N ILE D 524 " --> pdb=" O GLN D 520 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N TYR D 525 " --> pdb=" O HIS D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 559 removed outlier: 3.615A pdb=" N LEU D 538 " --> pdb=" O LEU D 534 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG D 539 " --> pdb=" O ARG D 535 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL D 543 " --> pdb=" O ARG D 539 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE D 547 " --> pdb=" O VAL D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 605 removed outlier: 3.914A pdb=" N PHE D 603 " --> pdb=" O GLU D 599 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N THR D 604 " --> pdb=" O LEU D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 650 removed outlier: 3.999A pdb=" N GLU D 647 " --> pdb=" O ALA D 643 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N THR D 648 " --> pdb=" O LEU D 644 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL D 649 " --> pdb=" O MET D 645 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASN D 650 " --> pdb=" O SER D 646 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 673 removed outlier: 4.002A pdb=" N TRP D 657 " --> pdb=" O ALA D 653 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASN D 673 " --> pdb=" O LEU D 669 " (cutoff:3.500A) Processing helix chain 'D' and resid 711 through 719 Processing sheet with id=AA1, first strand: chain 'A' and resid 329 through 335 removed outlier: 6.908A pdb=" N VAL A 340 " --> pdb=" O GLU A 332 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N CYS A 334 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL A 338 " --> pdb=" O CYS A 334 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 329 through 335 removed outlier: 6.908A pdb=" N VAL B 340 " --> pdb=" O GLU B 332 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N CYS B 334 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL B 338 " --> pdb=" O CYS B 334 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 329 through 335 removed outlier: 6.908A pdb=" N VAL C 340 " --> pdb=" O GLU C 332 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N CYS C 334 " --> pdb=" O VAL C 338 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL C 338 " --> pdb=" O CYS C 334 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 329 through 335 removed outlier: 6.908A pdb=" N VAL D 340 " --> pdb=" O GLU D 332 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N CYS D 334 " --> pdb=" O VAL D 338 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL D 338 " --> pdb=" O CYS D 334 " (cutoff:3.500A) 1068 hydrogen bonds defined for protein. 3084 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: 5.66 Time building geometry restraints manager: 5.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3249 1.33 - 1.45: 5281 1.45 - 1.57: 10902 1.57 - 1.69: 24 1.69 - 1.81: 176 Bond restraints: 19632 Sorted by residual: bond pdb=" C17 RTO D 803 " pdb=" O19 RTO D 803 " ideal model delta sigma weight residual 1.256 1.346 -0.090 2.00e-02 2.50e+03 2.01e+01 bond pdb=" C17 RTO B 803 " pdb=" O19 RTO B 803 " ideal model delta sigma weight residual 1.256 1.346 -0.090 2.00e-02 2.50e+03 2.01e+01 bond pdb=" C17 RTO A 803 " pdb=" O19 RTO A 803 " ideal model delta sigma weight residual 1.256 1.346 -0.090 2.00e-02 2.50e+03 2.01e+01 bond pdb=" C17 RTO C 803 " pdb=" O19 RTO C 803 " ideal model delta sigma weight residual 1.256 1.344 -0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" C14 RTO B 803 " pdb=" C17 RTO B 803 " ideal model delta sigma weight residual 1.531 1.473 0.058 2.00e-02 2.50e+03 8.41e+00 ... (remaining 19627 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 25970 1.43 - 2.85: 448 2.85 - 4.28: 130 4.28 - 5.70: 41 5.70 - 7.13: 23 Bond angle restraints: 26612 Sorted by residual: angle pdb=" CA PRO C 261 " pdb=" N PRO C 261 " pdb=" CD PRO C 261 " ideal model delta sigma weight residual 112.00 105.07 6.93 1.40e+00 5.10e-01 2.45e+01 angle pdb=" CA PRO A 261 " pdb=" N PRO A 261 " pdb=" CD PRO A 261 " ideal model delta sigma weight residual 112.00 105.11 6.89 1.40e+00 5.10e-01 2.42e+01 angle pdb=" CA PRO B 261 " pdb=" N PRO B 261 " pdb=" CD PRO B 261 " ideal model delta sigma weight residual 112.00 105.11 6.89 1.40e+00 5.10e-01 2.42e+01 angle pdb=" CA PRO D 261 " pdb=" N PRO D 261 " pdb=" CD PRO D 261 " ideal model delta sigma weight residual 112.00 105.13 6.87 1.40e+00 5.10e-01 2.41e+01 angle pdb=" C PHE A 618 " pdb=" N ARG A 619 " pdb=" CA ARG A 619 " ideal model delta sigma weight residual 120.38 124.87 -4.49 1.37e+00 5.33e-01 1.07e+01 ... (remaining 26607 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.01: 10652 23.01 - 46.02: 740 46.02 - 69.03: 144 69.03 - 92.04: 24 92.04 - 115.06: 8 Dihedral angle restraints: 11568 sinusoidal: 4620 harmonic: 6948 Sorted by residual: dihedral pdb=" CA PHE D 209 " pdb=" C PHE D 209 " pdb=" N GLY D 210 " pdb=" CA GLY D 210 " ideal model delta harmonic sigma weight residual -180.00 -158.73 -21.27 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA PHE A 209 " pdb=" C PHE A 209 " pdb=" N GLY A 210 " pdb=" CA GLY A 210 " ideal model delta harmonic sigma weight residual -180.00 -158.77 -21.23 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA PHE C 209 " pdb=" C PHE C 209 " pdb=" N GLY C 210 " pdb=" CA GLY C 210 " ideal model delta harmonic sigma weight residual -180.00 -158.78 -21.22 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 11565 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 2248 0.036 - 0.073: 617 0.073 - 0.109: 133 0.109 - 0.146: 14 0.146 - 0.182: 8 Chirality restraints: 3020 Sorted by residual: chirality pdb=" CA PRO B 261 " pdb=" N PRO B 261 " pdb=" C PRO B 261 " pdb=" CB PRO B 261 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.31e-01 chirality pdb=" CA PRO D 261 " pdb=" N PRO D 261 " pdb=" C PRO D 261 " pdb=" CB PRO D 261 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.28e-01 chirality pdb=" CA PRO C 261 " pdb=" N PRO C 261 " pdb=" C PRO C 261 " pdb=" CB PRO C 261 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.21e-01 ... (remaining 3017 not shown) Planarity restraints: 3256 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 260 " -0.061 5.00e-02 4.00e+02 8.82e-02 1.24e+01 pdb=" N PRO C 261 " 0.152 5.00e-02 4.00e+02 pdb=" CA PRO C 261 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 261 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 260 " -0.061 5.00e-02 4.00e+02 8.81e-02 1.24e+01 pdb=" N PRO B 261 " 0.152 5.00e-02 4.00e+02 pdb=" CA PRO B 261 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 261 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 260 " -0.061 5.00e-02 4.00e+02 8.80e-02 1.24e+01 pdb=" N PRO A 261 " 0.152 5.00e-02 4.00e+02 pdb=" CA PRO A 261 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 261 " -0.049 5.00e-02 4.00e+02 ... (remaining 3253 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 5183 2.80 - 3.33: 18291 3.33 - 3.85: 31590 3.85 - 4.38: 38597 4.38 - 4.90: 65971 Nonbonded interactions: 159632 Sorted by model distance: nonbonded pdb=" ND2 ASN A 263 " pdb=" OE2 GLU D 716 " model vdw 2.279 3.120 nonbonded pdb=" OE2 GLU A 716 " pdb=" ND2 ASN B 263 " model vdw 2.289 3.120 nonbonded pdb=" OE2 GLU C 716 " pdb=" ND2 ASN D 263 " model vdw 2.309 3.120 nonbonded pdb=" OE2 GLU B 716 " pdb=" ND2 ASN C 263 " model vdw 2.309 3.120 nonbonded pdb=" OH TYR C 544 " pdb=" OH TYR C 629 " model vdw 2.320 3.040 ... (remaining 159627 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: 0.14 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } 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 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: 1.620 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: 0.020 Extract box with map and model: 0.730 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 40.980 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.090 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:10.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 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 : 0.003 0.106 19632 Z= 0.147 Angle : 0.562 7.129 26612 Z= 0.312 Chirality : 0.036 0.182 3020 Planarity : 0.004 0.088 3256 Dihedral : 16.148 115.056 7072 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.87 % Allowed : 16.36 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.17 (0.17), residues: 2336 helix: 0.34 (0.13), residues: 1400 sheet: -0.21 (0.50), residues: 112 loop : 0.02 (0.23), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 333 HIS 0.003 0.001 HIS B 313 PHE 0.009 0.001 PHE C 547 TYR 0.022 0.001 TYR D 228 ARG 0.005 0.000 ARG C 617 Details of bonding type rmsd hydrogen bonds : bond 0.25155 ( 1068) hydrogen bonds : angle 6.61413 ( 3084) covalent geometry : bond 0.00319 (19632) covalent geometry : angle 0.56188 (26612) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 296 time to evaluate : 2.088 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 637 LEU cc_start: 0.7702 (mm) cc_final: 0.7440 (mt) REVERT: B 496 TRP cc_start: 0.7136 (m100) cc_final: 0.6914 (m100) REVERT: C 496 TRP cc_start: 0.7130 (m100) cc_final: 0.6926 (m100) REVERT: C 637 LEU cc_start: 0.7707 (mm) cc_final: 0.7440 (mt) REVERT: D 496 TRP cc_start: 0.7122 (m100) cc_final: 0.6912 (m100) REVERT: D 637 LEU cc_start: 0.7717 (mm) cc_final: 0.7427 (mt) outliers start: 37 outliers final: 20 residues processed: 329 average time/residue: 0.9665 time to fit residues: 372.0777 Evaluate side-chains 285 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 265 time to evaluate : 2.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 557 SER Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 557 SER Chi-restraints excluded: chain D residue 631 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 199 optimal weight: 1.9990 chunk 178 optimal weight: 5.9990 chunk 99 optimal weight: 0.3980 chunk 61 optimal weight: 20.0000 chunk 120 optimal weight: 8.9990 chunk 95 optimal weight: 3.9990 chunk 184 optimal weight: 0.0770 chunk 71 optimal weight: 3.9990 chunk 112 optimal weight: 20.0000 chunk 137 optimal weight: 3.9990 chunk 214 optimal weight: 10.0000 overall best weight: 2.0944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 HIS A 316 GLN A 370 HIS A 639 ASN B 313 HIS B 316 GLN B 370 HIS B 639 ASN C 313 HIS C 370 HIS C 639 ASN D 313 HIS D 316 GLN D 370 HIS D 639 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.177755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.139785 restraints weight = 22223.014| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 2.08 r_work: 0.3479 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 19632 Z= 0.192 Angle : 0.558 5.560 26612 Z= 0.281 Chirality : 0.040 0.153 3020 Planarity : 0.004 0.039 3256 Dihedral : 9.485 109.092 2844 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 4.60 % Allowed : 12.98 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.17), residues: 2336 helix: 1.42 (0.13), residues: 1456 sheet: -0.26 (0.59), residues: 84 loop : 0.33 (0.24), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 333 HIS 0.006 0.001 HIS D 169 PHE 0.017 0.001 PHE B 547 TYR 0.011 0.002 TYR D 403 ARG 0.004 0.001 ARG C 458 Details of bonding type rmsd hydrogen bonds : bond 0.04541 ( 1068) hydrogen bonds : angle 3.81702 ( 3084) covalent geometry : bond 0.00462 (19632) covalent geometry : angle 0.55847 (26612) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 303 time to evaluate : 2.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 448 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8605 (mp) REVERT: A 637 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7414 (mt) REVERT: B 448 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8591 (mp) REVERT: B 457 TRP cc_start: 0.7545 (t60) cc_final: 0.7210 (t60) REVERT: B 637 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7406 (mt) REVERT: C 448 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8586 (mp) REVERT: C 457 TRP cc_start: 0.7579 (t60) cc_final: 0.7222 (t60) REVERT: C 637 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7416 (mt) REVERT: D 448 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8590 (mp) REVERT: D 457 TRP cc_start: 0.7573 (t60) cc_final: 0.7225 (t60) REVERT: D 637 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7410 (mt) outliers start: 91 outliers final: 44 residues processed: 357 average time/residue: 0.9567 time to fit residues: 400.9615 Evaluate side-chains 328 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 276 time to evaluate : 2.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 471 TYR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 471 TYR Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 691 VAL Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 471 TYR Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 471 TYR Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 691 VAL Chi-restraints excluded: chain D residue 709 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 142 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 chunk 198 optimal weight: 4.9990 chunk 62 optimal weight: 20.0000 chunk 166 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 167 optimal weight: 8.9990 chunk 211 optimal weight: 3.9990 chunk 12 optimal weight: 0.0000 chunk 0 optimal weight: 20.0000 chunk 110 optimal weight: 0.9990 overall best weight: 1.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS A 414 GLN A 487 GLN B 165 HIS B 414 GLN B 487 GLN C 165 HIS C 414 GLN C 487 GLN D 414 GLN D 487 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.178151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.140042 restraints weight = 22219.862| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.04 r_work: 0.3494 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 19632 Z= 0.151 Angle : 0.505 5.690 26612 Z= 0.253 Chirality : 0.039 0.153 3020 Planarity : 0.004 0.039 3256 Dihedral : 8.883 101.536 2824 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 3.74 % Allowed : 16.06 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 1.73 (0.18), residues: 2336 helix: 1.72 (0.13), residues: 1444 sheet: -0.12 (0.51), residues: 112 loop : 0.41 (0.24), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 333 HIS 0.004 0.001 HIS C 169 PHE 0.014 0.001 PHE C 547 TYR 0.016 0.001 TYR D 228 ARG 0.003 0.000 ARG C 458 Details of bonding type rmsd hydrogen bonds : bond 0.03646 ( 1068) hydrogen bonds : angle 3.57598 ( 3084) covalent geometry : bond 0.00362 (19632) covalent geometry : angle 0.50546 (26612) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 299 time to evaluate : 2.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 435 LEU cc_start: 0.7059 (OUTLIER) cc_final: 0.6824 (tp) REVERT: A 448 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8570 (mp) REVERT: A 637 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7470 (mt) REVERT: B 435 LEU cc_start: 0.7075 (OUTLIER) cc_final: 0.6849 (tp) REVERT: B 448 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8558 (mp) REVERT: B 637 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7394 (mt) REVERT: C 435 LEU cc_start: 0.7071 (OUTLIER) cc_final: 0.6847 (tp) REVERT: C 448 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8568 (mp) REVERT: C 637 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7443 (mt) REVERT: D 435 LEU cc_start: 0.7075 (OUTLIER) cc_final: 0.6846 (tp) REVERT: D 448 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8552 (mp) REVERT: D 637 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7438 (mt) outliers start: 74 outliers final: 24 residues processed: 346 average time/residue: 0.8751 time to fit residues: 357.6331 Evaluate side-chains 316 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 280 time to evaluate : 2.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 685 GLU Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 685 GLU Chi-restraints excluded: chain B residue 691 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 685 GLU Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 685 GLU Chi-restraints excluded: chain D residue 691 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 213 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 63 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 66 optimal weight: 0.1980 chunk 152 optimal weight: 8.9990 chunk 131 optimal weight: 1.9990 chunk 147 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN C 452 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.181562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.143254 restraints weight = 22370.353| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 2.08 r_work: 0.3532 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 19632 Z= 0.094 Angle : 0.469 9.235 26612 Z= 0.230 Chirality : 0.037 0.163 3020 Planarity : 0.003 0.039 3256 Dihedral : 8.285 82.903 2824 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 4.14 % Allowed : 16.87 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.18), residues: 2336 helix: 2.05 (0.14), residues: 1448 sheet: -0.08 (0.50), residues: 112 loop : 0.32 (0.24), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 333 HIS 0.003 0.001 HIS B 269 PHE 0.011 0.001 PHE B 547 TYR 0.012 0.001 TYR A 228 ARG 0.002 0.000 ARG C 458 Details of bonding type rmsd hydrogen bonds : bond 0.03017 ( 1068) hydrogen bonds : angle 3.35382 ( 3084) covalent geometry : bond 0.00212 (19632) covalent geometry : angle 0.46925 (26612) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 286 time to evaluate : 2.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 CYS cc_start: 0.7429 (m) cc_final: 0.7061 (m) REVERT: A 435 LEU cc_start: 0.7104 (OUTLIER) cc_final: 0.6851 (tp) REVERT: A 448 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8463 (mp) REVERT: A 637 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7357 (mt) REVERT: B 435 LEU cc_start: 0.7161 (OUTLIER) cc_final: 0.6902 (tp) REVERT: B 448 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8532 (mp) REVERT: B 637 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7344 (mt) REVERT: C 435 LEU cc_start: 0.7163 (OUTLIER) cc_final: 0.6904 (tp) REVERT: C 448 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8462 (mp) REVERT: C 536 ASP cc_start: 0.7256 (t70) cc_final: 0.6824 (m-30) REVERT: C 637 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7376 (mt) REVERT: D 179 CYS cc_start: 0.7443 (m) cc_final: 0.7077 (m) REVERT: D 435 LEU cc_start: 0.7164 (OUTLIER) cc_final: 0.6903 (tp) REVERT: D 448 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8544 (mp) REVERT: D 637 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7381 (mt) outliers start: 82 outliers final: 36 residues processed: 344 average time/residue: 0.9142 time to fit residues: 379.2326 Evaluate side-chains 315 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 267 time to evaluate : 2.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 685 GLU Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 471 TYR Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 685 GLU Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 263 ASN Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 471 TYR Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 685 GLU Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 263 ASN Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 471 TYR Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 685 GLU Chi-restraints excluded: chain D residue 709 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 37 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 188 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 chunk 193 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 206 optimal weight: 0.0050 chunk 215 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 3 optimal weight: 0.0030 chunk 218 optimal weight: 0.2980 overall best weight: 0.4406 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.183052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.145308 restraints weight = 22453.992| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 2.05 r_work: 0.3567 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 19632 Z= 0.086 Angle : 0.461 8.839 26612 Z= 0.225 Chirality : 0.037 0.164 3020 Planarity : 0.003 0.039 3256 Dihedral : 7.995 64.651 2824 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.68 % Allowed : 18.23 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.18), residues: 2336 helix: 2.18 (0.14), residues: 1460 sheet: -0.12 (0.48), residues: 112 loop : 0.39 (0.24), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 333 HIS 0.003 0.001 HIS D 269 PHE 0.007 0.001 PHE C 311 TYR 0.014 0.001 TYR C 228 ARG 0.002 0.000 ARG D 617 Details of bonding type rmsd hydrogen bonds : bond 0.02829 ( 1068) hydrogen bonds : angle 3.20591 ( 3084) covalent geometry : bond 0.00183 (19632) covalent geometry : angle 0.46136 (26612) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 284 time to evaluate : 2.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.7475 (ttm) cc_final: 0.7267 (mtt) REVERT: A 435 LEU cc_start: 0.7072 (OUTLIER) cc_final: 0.6814 (tp) REVERT: A 448 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8456 (mp) REVERT: A 637 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7372 (mt) REVERT: B 122 MET cc_start: 0.7488 (ttm) cc_final: 0.7277 (mtt) REVERT: B 435 LEU cc_start: 0.7083 (OUTLIER) cc_final: 0.6831 (tp) REVERT: B 448 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8457 (mp) REVERT: B 539 ARG cc_start: 0.8678 (mpp80) cc_final: 0.8425 (tpp80) REVERT: B 637 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7309 (mt) REVERT: C 106 LEU cc_start: 0.6952 (mp) cc_final: 0.6527 (mt) REVERT: C 139 LEU cc_start: 0.7930 (tp) cc_final: 0.7623 (mt) REVERT: C 435 LEU cc_start: 0.7075 (OUTLIER) cc_final: 0.6821 (tp) REVERT: C 448 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8451 (mp) REVERT: C 637 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7391 (mt) REVERT: D 106 LEU cc_start: 0.7029 (mp) cc_final: 0.6641 (mt) REVERT: D 122 MET cc_start: 0.7534 (mtm) cc_final: 0.7289 (mtt) REVERT: D 435 LEU cc_start: 0.7081 (OUTLIER) cc_final: 0.6827 (tp) REVERT: D 448 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8456 (mp) REVERT: D 637 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7358 (mt) outliers start: 53 outliers final: 34 residues processed: 321 average time/residue: 0.9263 time to fit residues: 348.1743 Evaluate side-chains 315 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 269 time to evaluate : 1.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 685 GLU Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 471 TYR Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 685 GLU Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 263 ASN Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 685 GLU Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 263 ASN Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 471 TYR Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 685 GLU Chi-restraints excluded: chain D residue 709 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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: 58.6333 > 50: distance: 22 - 26: 14.399 distance: 26 - 27: 10.785 distance: 27 - 28: 16.166 distance: 27 - 30: 17.663 distance: 28 - 29: 11.603 distance: 28 - 35: 29.832 distance: 30 - 31: 21.954 distance: 31 - 32: 10.617 distance: 32 - 34: 15.724 distance: 35 - 36: 36.597 distance: 35 - 41: 9.830 distance: 36 - 37: 5.124 distance: 36 - 39: 23.096 distance: 37 - 38: 40.388 distance: 39 - 40: 17.410 distance: 40 - 41: 50.053 distance: 42 - 43: 45.602 distance: 43 - 44: 16.248 distance: 44 - 45: 7.049 distance: 44 - 46: 16.880 distance: 46 - 47: 3.863 distance: 47 - 48: 12.552 distance: 47 - 50: 27.540 distance: 48 - 49: 24.233 distance: 48 - 51: 30.468 distance: 49 - 72: 14.790 distance: 51 - 52: 16.743 distance: 52 - 53: 17.058 distance: 52 - 55: 23.672 distance: 53 - 54: 20.254 distance: 53 - 56: 19.914 distance: 54 - 80: 12.953 distance: 56 - 57: 14.388 distance: 57 - 58: 7.057 distance: 57 - 60: 9.689 distance: 58 - 59: 3.559 distance: 58 - 64: 6.845 distance: 59 - 88: 16.005 distance: 60 - 61: 8.012 distance: 61 - 62: 45.964 distance: 62 - 63: 30.865 distance: 64 - 65: 5.992 distance: 65 - 66: 12.437 distance: 65 - 68: 13.317 distance: 66 - 67: 13.401 distance: 66 - 72: 11.523 distance: 67 - 92: 17.323 distance: 68 - 69: 8.301 distance: 69 - 70: 39.424 distance: 69 - 71: 4.999 distance: 72 - 73: 8.691 distance: 73 - 74: 7.148 distance: 73 - 76: 9.654 distance: 74 - 75: 10.639 distance: 74 - 80: 19.624 distance: 75 - 102: 4.879 distance: 76 - 77: 12.125 distance: 77 - 78: 22.870 distance: 77 - 79: 9.337 distance: 80 - 81: 13.347 distance: 81 - 82: 8.613 distance: 81 - 84: 13.383 distance: 82 - 83: 6.765 distance: 82 - 88: 4.115 distance: 83 - 110: 26.094 distance: 84 - 85: 20.538 distance: 85 - 86: 3.900 distance: 85 - 87: 18.967 distance: 89 - 90: 9.750 distance: 90 - 91: 26.827 distance: 90 - 92: 14.791 distance: 91 - 118: 19.403