Starting phenix.real_space_refine on Mon Jun 16 19:29:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b3z_44161/06_2025/9b3z_44161.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b3z_44161/06_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_44161/06_2025/9b3z_44161.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b3z_44161/06_2025/9b3z_44161.map" model { file = "/net/cci-nas-00/data/ceres_data/9b3z_44161/06_2025/9b3z_44161.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b3z_44161/06_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 11.35, per 1000 atoms: 0.59 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: 5.23 Conformation dependent library (CDL) restraints added in 2.3 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: 1.99 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: 5.41 Time building geometry restraints manager: 6.07 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: 1.800 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: 0.830 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 42.980 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.870 ------------------------------------------------------------------------------- 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 : 2.038 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: 0.9970 time to fit residues: 383.0294 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 : 2.096 ------------------------------------------------------------------------------- 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 = 0.139782 restraints weight = 22223.014| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 2.08 r_work: 0.3479 rms_B_bonded: 3.11 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 : 2.125 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: 0.8815 (OUTLIER) cc_final: 0.8604 (mp) REVERT: A 637 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7408 (mt) REVERT: B 448 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8590 (mp) REVERT: B 457 TRP cc_start: 0.7540 (t60) cc_final: 0.7208 (t60) REVERT: B 637 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7398 (mt) REVERT: C 448 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8585 (mp) REVERT: C 457 TRP cc_start: 0.7575 (t60) cc_final: 0.7219 (t60) REVERT: C 637 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7406 (mt) REVERT: D 448 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8589 (mp) REVERT: D 457 TRP cc_start: 0.7569 (t60) cc_final: 0.7223 (t60) REVERT: D 637 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7405 (mt) outliers start: 91 outliers final: 44 residues processed: 357 average time/residue: 1.1619 time to fit residues: 485.0922 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 : 2.607 ------------------------------------------------------------------------------- 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: 5.9990 chunk 62 optimal weight: 20.0000 chunk 166 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 167 optimal weight: 6.9990 chunk 211 optimal weight: 4.9990 chunk 12 optimal weight: 0.0000 chunk 0 optimal weight: 20.0000 chunk 110 optimal weight: 0.9980 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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 = 0.178128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.140012 restraints weight = 22224.917| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 2.04 r_work: 0.3493 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1984 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 : 0.506 5.606 26612 Z= 0.253 Chirality : 0.039 0.157 3020 Planarity : 0.004 0.039 3256 Dihedral : 8.902 101.953 2824 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 3.89 % Allowed : 16.11 % Favored : 80.00 % 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 0.017 0.001 TRP B 333 HIS 0.004 0.001 HIS C 169 PHE 0.015 0.001 PHE A 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 0.03682 ( 1068) hydrogen bonds : angle 3.58521 ( 3084) covalent geometry : bond 0.00362 (19632) covalent geometry : angle 0.50624 (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 375 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 298 time to evaluate : 2.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 LEU cc_start: 0.7534 (tt) cc_final: 0.7317 (tt) REVERT: A 435 LEU cc_start: 0.7058 (OUTLIER) cc_final: 0.6823 (tp) REVERT: A 448 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8571 (mp) REVERT: A 637 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7446 (mt) REVERT: B 435 LEU cc_start: 0.7069 (OUTLIER) cc_final: 0.6845 (tp) REVERT: B 448 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8556 (mp) REVERT: B 637 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7373 (mt) REVERT: C 182 LEU cc_start: 0.7570 (tt) cc_final: 0.7313 (tt) REVERT: C 435 LEU cc_start: 0.7070 (OUTLIER) cc_final: 0.6844 (tp) REVERT: C 448 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8563 (mp) REVERT: C 637 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7411 (mt) REVERT: D 435 LEU cc_start: 0.7068 (OUTLIER) cc_final: 0.6840 (tp) REVERT: D 448 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8556 (mp) REVERT: D 637 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7415 (mt) outliers start: 77 outliers final: 27 residues processed: 348 average time/residue: 0.9283 time to fit residues: 380.3998 Evaluate side-chains 316 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 277 time to evaluate : 2.112 ------------------------------------------------------------------------------- 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 126 LEU 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 631 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 631 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: 0.9990 chunk 14 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 63 optimal weight: 5.9990 chunk 31 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 152 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 chunk 147 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.4149 r_free = 0.4149 target = 0.180937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.142792 restraints weight = 22329.339| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 2.06 r_work: 0.3526 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 19632 Z= 0.100 Angle : 0.467 8.662 26612 Z= 0.230 Chirality : 0.037 0.191 3020 Planarity : 0.003 0.040 3256 Dihedral : 8.340 85.451 2824 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 4.14 % Allowed : 16.82 % Favored : 79.04 % 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: 2.01 (0.18), residues: 2336 helix: 2.03 (0.14), residues: 1448 sheet: -0.09 (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 0.013 0.001 TYR B 228 ARG 0.002 0.000 ARG C 458 Details of bonding type rmsd hydrogen bonds : bond 0.03072 ( 1068) hydrogen bonds : angle 3.37832 ( 3084) covalent geometry : bond 0.00230 (19632) covalent geometry : angle 0.46713 (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 : 2.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 CYS cc_start: 0.7449 (m) cc_final: 0.7072 (m) REVERT: A 435 LEU cc_start: 0.7104 (OUTLIER) cc_final: 0.6854 (tp) REVERT: A 448 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8523 (mp) REVERT: A 637 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7353 (mt) REVERT: B 435 LEU cc_start: 0.7165 (OUTLIER) cc_final: 0.6909 (tp) REVERT: B 448 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8531 (mp) REVERT: B 637 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7337 (mt) REVERT: C 435 LEU cc_start: 0.7165 (OUTLIER) cc_final: 0.6907 (tp) REVERT: C 448 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8526 (mp) REVERT: C 637 LEU cc_start: 0.7804 (OUTLIER) cc_final: 0.7381 (mt) REVERT: D 179 CYS cc_start: 0.7428 (m) cc_final: 0.7059 (m) REVERT: D 435 LEU cc_start: 0.7167 (OUTLIER) cc_final: 0.6905 (tp) REVERT: D 448 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8530 (mp) REVERT: D 637 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.7377 (mt) outliers start: 82 outliers final: 35 residues processed: 342 average time/residue: 0.8662 time to fit residues: 354.3008 Evaluate side-chains 314 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 267 time to evaluate : 2.008 ------------------------------------------------------------------------------- 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 471 TYR 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 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 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: 8.9990 chunk 139 optimal weight: 2.9990 chunk 188 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 193 optimal weight: 10.0000 chunk 100 optimal weight: 0.5980 chunk 206 optimal weight: 0.7980 chunk 215 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 3 optimal weight: 6.9990 chunk 218 optimal weight: 0.0050 overall best weight: 0.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 452 GLN D 165 HIS D 452 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.181070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.142936 restraints weight = 22491.374| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 2.06 r_work: 0.3527 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 19632 Z= 0.106 Angle : 0.478 9.015 26612 Z= 0.235 Chirality : 0.038 0.195 3020 Planarity : 0.003 0.040 3256 Dihedral : 8.204 80.375 2824 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.33 % Allowed : 18.03 % Favored : 78.64 % 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: 2.06 (0.18), residues: 2336 helix: 2.07 (0.14), residues: 1456 sheet: -0.20 (0.49), residues: 112 loop : 0.34 (0.24), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 333 HIS 0.003 0.001 HIS D 269 PHE 0.010 0.001 PHE A 547 TYR 0.013 0.001 TYR D 228 ARG 0.002 0.000 ARG B 458 Details of bonding type rmsd hydrogen bonds : bond 0.03073 ( 1068) hydrogen bonds : angle 3.30009 ( 3084) covalent geometry : bond 0.00245 (19632) covalent geometry : angle 0.47843 (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 344 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 278 time to evaluate : 2.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 435 LEU cc_start: 0.7110 (OUTLIER) cc_final: 0.6858 (tp) REVERT: A 448 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8525 (mp) REVERT: A 637 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7360 (mt) REVERT: B 122 MET cc_start: 0.7604 (mtm) cc_final: 0.7335 (mtm) REVERT: B 435 LEU cc_start: 0.7139 (OUTLIER) cc_final: 0.6891 (tp) REVERT: B 448 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8508 (mp) REVERT: B 637 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7350 (mt) REVERT: C 106 LEU cc_start: 0.6976 (mp) cc_final: 0.6662 (mt) REVERT: C 122 MET cc_start: 0.7522 (OUTLIER) cc_final: 0.7260 (ttm) REVERT: C 435 LEU cc_start: 0.7127 (OUTLIER) cc_final: 0.6882 (tp) REVERT: C 448 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8524 (mp) REVERT: C 637 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7369 (mt) REVERT: D 106 LEU cc_start: 0.7055 (mp) cc_final: 0.6733 (mt) REVERT: D 122 MET cc_start: 0.7558 (OUTLIER) cc_final: 0.7345 (mtt) REVERT: D 435 LEU cc_start: 0.7136 (OUTLIER) cc_final: 0.6888 (tp) REVERT: D 448 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8505 (mp) REVERT: D 637 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7368 (mt) outliers start: 66 outliers final: 38 residues processed: 320 average time/residue: 0.9324 time to fit residues: 351.9848 Evaluate side-chains 321 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 269 time to evaluate : 2.213 ------------------------------------------------------------------------------- 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 624 LEU 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 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 358 GLU 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 541 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 B residue 709 GLU Chi-restraints excluded: chain C residue 122 MET 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 691 VAL Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain D residue 122 MET 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 358 GLU 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 541 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 Chi-restraints excluded: chain D residue 709 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 83 optimal weight: 0.0070 chunk 43 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 211 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 overall best weight: 1.3404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN B 247 ASN C 247 ASN D 247 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.179217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.141014 restraints weight = 22559.556| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.04 r_work: 0.3500 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 19632 Z= 0.131 Angle : 0.494 9.735 26612 Z= 0.241 Chirality : 0.038 0.171 3020 Planarity : 0.003 0.040 3256 Dihedral : 8.301 86.222 2824 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.59 % Allowed : 18.54 % Favored : 77.88 % 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: 1.97 (0.18), residues: 2336 helix: 2.01 (0.14), residues: 1456 sheet: -0.33 (0.48), residues: 112 loop : 0.30 (0.24), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 333 HIS 0.004 0.001 HIS A 169 PHE 0.009 0.001 PHE C 547 TYR 0.009 0.001 TYR A 228 ARG 0.002 0.000 ARG D 539 Details of bonding type rmsd hydrogen bonds : bond 0.03216 ( 1068) hydrogen bonds : angle 3.33878 ( 3084) covalent geometry : bond 0.00312 (19632) covalent geometry : angle 0.49369 (26612) *********************** REFINEMENT MACRO_CYCLE 6 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 345 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 274 time to evaluate : 2.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 448 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8557 (mp) REVERT: A 539 ARG cc_start: 0.8912 (OUTLIER) cc_final: 0.8263 (mpp80) REVERT: A 637 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7394 (mt) REVERT: B 448 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8552 (mp) REVERT: B 539 ARG cc_start: 0.8876 (OUTLIER) cc_final: 0.8142 (mpp80) REVERT: B 637 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7407 (mt) REVERT: C 106 LEU cc_start: 0.6960 (mp) cc_final: 0.6658 (mt) REVERT: C 448 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8550 (mp) REVERT: C 637 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7404 (mt) REVERT: D 106 LEU cc_start: 0.6997 (mp) cc_final: 0.6699 (mt) REVERT: D 448 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8557 (mp) REVERT: D 637 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7430 (mt) outliers start: 71 outliers final: 41 residues processed: 319 average time/residue: 0.9385 time to fit residues: 351.6006 Evaluate side-chains 316 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 265 time to evaluate : 2.152 ------------------------------------------------------------------------------- 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 358 GLU 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 494 THR Chi-restraints excluded: chain A residue 539 ARG Chi-restraints excluded: chain A residue 624 LEU 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 158 THR Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 358 GLU 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 539 ARG 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 158 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 263 ASN Chi-restraints excluded: chain C residue 358 GLU 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 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 158 THR Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 263 ASN Chi-restraints excluded: chain D residue 358 GLU 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 485 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 209 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 159 optimal weight: 0.7980 chunk 203 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 126 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 139 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 = 0.4116 r_free = 0.4116 target = 0.177902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.139570 restraints weight = 22364.799| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 2.05 r_work: 0.3482 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 19632 Z= 0.161 Angle : 0.532 9.826 26612 Z= 0.259 Chirality : 0.039 0.207 3020 Planarity : 0.004 0.041 3256 Dihedral : 8.598 97.315 2824 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.28 % Allowed : 19.29 % Favored : 77.42 % 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: 1.87 (0.18), residues: 2336 helix: 1.92 (0.14), residues: 1456 sheet: -0.36 (0.49), residues: 112 loop : 0.28 (0.24), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 333 HIS 0.004 0.001 HIS B 169 PHE 0.009 0.001 PHE D 705 TYR 0.017 0.001 TYR C 228 ARG 0.002 0.000 ARG C 459 Details of bonding type rmsd hydrogen bonds : bond 0.03398 ( 1068) hydrogen bonds : angle 3.40833 ( 3084) covalent geometry : bond 0.00387 (19632) covalent geometry : angle 0.53188 (26612) *********************** REFINEMENT MACRO_CYCLE 7 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 338 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 273 time to evaluate : 2.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 448 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8522 (mp) REVERT: A 457 TRP cc_start: 0.7625 (t60) cc_final: 0.7266 (t60) REVERT: A 539 ARG cc_start: 0.8916 (OUTLIER) cc_final: 0.8261 (mpp80) REVERT: A 637 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7410 (mt) REVERT: B 448 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8527 (mp) REVERT: B 457 TRP cc_start: 0.7644 (t60) cc_final: 0.7238 (t60) REVERT: B 539 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8178 (mpp80) REVERT: B 637 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7409 (mt) REVERT: C 106 LEU cc_start: 0.6965 (mp) cc_final: 0.6577 (mt) REVERT: C 448 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8524 (mp) REVERT: C 457 TRP cc_start: 0.7627 (t60) cc_final: 0.7266 (t60) REVERT: C 637 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7436 (mt) REVERT: D 106 LEU cc_start: 0.7011 (mp) cc_final: 0.6627 (mt) REVERT: D 448 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8529 (mp) REVERT: D 457 TRP cc_start: 0.7644 (t60) cc_final: 0.7241 (t60) REVERT: D 637 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7461 (mt) outliers start: 65 outliers final: 43 residues processed: 318 average time/residue: 1.0915 time to fit residues: 408.2272 Evaluate side-chains 324 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 271 time to evaluate : 3.638 ------------------------------------------------------------------------------- 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 358 GLU 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 494 THR Chi-restraints excluded: chain A residue 539 ARG Chi-restraints excluded: chain A residue 624 LEU 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 158 THR Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 358 GLU 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 485 LEU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 539 ARG 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 158 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 263 ASN Chi-restraints excluded: chain C residue 358 GLU 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 485 LEU 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 158 THR Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 263 ASN Chi-restraints excluded: chain D residue 358 GLU 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 485 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 133 optimal weight: 2.9990 chunk 194 optimal weight: 0.0030 chunk 37 optimal weight: 0.6980 chunk 182 optimal weight: 0.3980 chunk 163 optimal weight: 0.9990 chunk 49 optimal weight: 9.9990 chunk 169 optimal weight: 0.9980 chunk 230 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 127 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 HIS C 269 HIS D 269 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.181899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.143786 restraints weight = 22468.792| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 2.05 r_work: 0.3544 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 19632 Z= 0.089 Angle : 0.471 9.950 26612 Z= 0.229 Chirality : 0.036 0.176 3020 Planarity : 0.003 0.040 3256 Dihedral : 8.053 76.065 2824 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.13 % Allowed : 19.44 % Favored : 77.42 % 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: 2.18 (0.18), residues: 2336 helix: 2.24 (0.14), residues: 1448 sheet: -0.29 (0.48), residues: 112 loop : 0.27 (0.23), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 333 HIS 0.003 0.001 HIS B 269 PHE 0.011 0.001 PHE C 547 TYR 0.020 0.001 TYR C 228 ARG 0.002 0.000 ARG D 458 Details of bonding type rmsd hydrogen bonds : bond 0.02781 ( 1068) hydrogen bonds : angle 3.21899 ( 3084) covalent geometry : bond 0.00196 (19632) covalent geometry : angle 0.47084 (26612) *********************** REFINEMENT MACRO_CYCLE 8 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 339 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 277 time to evaluate : 4.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 448 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8524 (mp) REVERT: A 539 ARG cc_start: 0.8827 (OUTLIER) cc_final: 0.8179 (mpp80) REVERT: A 637 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7395 (mt) REVERT: B 435 LEU cc_start: 0.7050 (OUTLIER) cc_final: 0.6818 (tp) REVERT: B 448 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8520 (mp) REVERT: B 539 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.8027 (mpp80) REVERT: B 637 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7380 (mt) REVERT: C 106 LEU cc_start: 0.6950 (mp) cc_final: 0.6502 (mt) REVERT: C 435 LEU cc_start: 0.7036 (OUTLIER) cc_final: 0.6806 (tp) REVERT: C 448 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8524 (mp) REVERT: C 539 ARG cc_start: 0.8828 (OUTLIER) cc_final: 0.8137 (mpp80) REVERT: C 637 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7416 (mt) REVERT: D 106 LEU cc_start: 0.6972 (mp) cc_final: 0.6519 (mt) REVERT: D 448 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8522 (mp) REVERT: D 539 ARG cc_start: 0.8875 (OUTLIER) cc_final: 0.8176 (mpp80) REVERT: D 637 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.7426 (mt) outliers start: 62 outliers final: 35 residues processed: 318 average time/residue: 1.0758 time to fit residues: 401.1549 Evaluate side-chains 310 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 261 time to evaluate : 2.160 ------------------------------------------------------------------------------- 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 448 LEU Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 539 ARG 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 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 539 ARG 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 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 539 ARG 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 158 THR Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 263 ASN 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 485 LEU Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 539 ARG 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 71 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 76 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 chunk 181 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 75 optimal weight: 0.0470 chunk 89 optimal weight: 1.9990 chunk 99 optimal weight: 0.0770 chunk 198 optimal weight: 6.9990 chunk 125 optimal weight: 1.9990 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN B 269 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.181676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.143345 restraints weight = 22563.417| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 2.22 r_work: 0.3524 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 19632 Z= 0.097 Angle : 0.495 10.558 26612 Z= 0.236 Chirality : 0.038 0.204 3020 Planarity : 0.003 0.040 3256 Dihedral : 8.040 68.524 2824 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.68 % Allowed : 20.45 % Favored : 76.87 % 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: 2.12 (0.18), residues: 2336 helix: 2.20 (0.14), residues: 1456 sheet: -0.24 (0.48), residues: 112 loop : 0.18 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 333 HIS 0.003 0.001 HIS A 269 PHE 0.008 0.001 PHE C 547 TYR 0.014 0.001 TYR C 228 ARG 0.001 0.000 ARG D 459 Details of bonding type rmsd hydrogen bonds : bond 0.02906 ( 1068) hydrogen bonds : angle 3.22406 ( 3084) covalent geometry : bond 0.00219 (19632) covalent geometry : angle 0.49474 (26612) *********************** REFINEMENT MACRO_CYCLE 9 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 321 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 268 time to evaluate : 2.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 433 MET cc_start: 0.7734 (tpp) cc_final: 0.6154 (tpt) REVERT: A 448 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8524 (mp) REVERT: A 539 ARG cc_start: 0.8843 (OUTLIER) cc_final: 0.8202 (mpp80) REVERT: A 637 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7385 (mt) REVERT: B 448 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8522 (mp) REVERT: B 539 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.8128 (mpp80) REVERT: B 637 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7364 (mt) REVERT: C 106 LEU cc_start: 0.6882 (mp) cc_final: 0.6444 (mt) REVERT: C 448 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8514 (mp) REVERT: C 539 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.8166 (mpp80) REVERT: C 637 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7365 (mt) REVERT: D 106 LEU cc_start: 0.6899 (mp) cc_final: 0.6457 (mt) REVERT: D 433 MET cc_start: 0.7727 (tpp) cc_final: 0.6151 (tpt) REVERT: D 448 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8523 (mp) REVERT: D 539 ARG cc_start: 0.8886 (OUTLIER) cc_final: 0.8208 (mpp80) REVERT: D 637 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7403 (mt) outliers start: 53 outliers final: 36 residues processed: 306 average time/residue: 1.0216 time to fit residues: 366.5119 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 : 2.134 ------------------------------------------------------------------------------- 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 448 LEU Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 539 ARG 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 158 THR Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 263 ASN 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 539 ARG 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 685 GLU Chi-restraints excluded: chain B residue 691 VAL 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 448 LEU Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 539 ARG 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 158 THR Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 263 ASN 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 485 LEU Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 539 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 36 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 179 optimal weight: 8.9990 chunk 65 optimal weight: 4.9990 chunk 120 optimal weight: 8.9990 chunk 109 optimal weight: 2.9990 chunk 210 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 203 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN A 269 HIS A 414 GLN B 414 GLN C 269 HIS C 414 GLN D 269 HIS D 414 GLN D 487 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.177566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.138975 restraints weight = 22443.058| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.06 r_work: 0.3473 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 19632 Z= 0.192 Angle : 0.576 10.504 26612 Z= 0.275 Chirality : 0.040 0.204 3020 Planarity : 0.004 0.040 3256 Dihedral : 8.655 92.921 2824 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.63 % Allowed : 20.30 % Favored : 77.07 % 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: 1.74 (0.18), residues: 2336 helix: 1.89 (0.14), residues: 1456 sheet: -0.31 (0.50), residues: 112 loop : 0.05 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 333 HIS 0.005 0.001 HIS B 169 PHE 0.016 0.001 PHE C 547 TYR 0.016 0.002 TYR A 412 ARG 0.002 0.000 ARG A 459 Details of bonding type rmsd hydrogen bonds : bond 0.03590 ( 1068) hydrogen bonds : angle 3.50729 ( 3084) covalent geometry : bond 0.00466 (19632) covalent geometry : angle 0.57626 (26612) ********************** REFINEMENT MACRO_CYCLE 10 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 320 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 268 time to evaluate : 2.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 433 MET cc_start: 0.7782 (tpp) cc_final: 0.6180 (tpt) REVERT: A 448 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8471 (mp) REVERT: A 457 TRP cc_start: 0.7642 (t60) cc_final: 0.7226 (t60) REVERT: A 539 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.8250 (mpp80) REVERT: A 637 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7419 (mt) REVERT: A 645 MET cc_start: 0.7841 (ttm) cc_final: 0.7567 (ttt) REVERT: B 448 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8466 (mp) REVERT: B 457 TRP cc_start: 0.7639 (t60) cc_final: 0.7225 (t60) REVERT: B 539 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.8183 (mpp80) REVERT: B 637 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7421 (mt) REVERT: C 106 LEU cc_start: 0.6837 (mp) cc_final: 0.6423 (mt) REVERT: C 448 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8460 (mp) REVERT: C 457 TRP cc_start: 0.7646 (t60) cc_final: 0.7227 (t60) REVERT: C 539 ARG cc_start: 0.8910 (OUTLIER) cc_final: 0.8293 (mpp80) REVERT: C 637 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7431 (mt) REVERT: D 106 LEU cc_start: 0.6881 (mp) cc_final: 0.6440 (mt) REVERT: D 433 MET cc_start: 0.7783 (tpp) cc_final: 0.6182 (tpt) REVERT: D 448 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8472 (mp) REVERT: D 457 TRP cc_start: 0.7638 (t60) cc_final: 0.7226 (t60) REVERT: D 539 ARG cc_start: 0.8913 (OUTLIER) cc_final: 0.8264 (mpp80) REVERT: D 637 LEU cc_start: 0.7832 (OUTLIER) cc_final: 0.7454 (mt) REVERT: D 645 MET cc_start: 0.7424 (mmt) cc_final: 0.7109 (mmm) outliers start: 52 outliers final: 35 residues processed: 305 average time/residue: 0.9814 time to fit residues: 348.9720 Evaluate side-chains 310 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 263 time to evaluate : 2.030 ------------------------------------------------------------------------------- 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 448 LEU Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 471 TYR Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 539 ARG Chi-restraints excluded: chain A residue 624 LEU 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 158 THR Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 263 ASN 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 539 ARG 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 158 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 263 ASN 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 537 LEU Chi-restraints excluded: chain C residue 539 ARG 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 158 THR Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 263 ASN Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 539 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 173 optimal weight: 0.9990 chunk 174 optimal weight: 4.9990 chunk 175 optimal weight: 0.9980 chunk 156 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 193 optimal weight: 0.8980 chunk 162 optimal weight: 0.8980 chunk 160 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 207 optimal weight: 0.6980 chunk 154 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 HIS ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 269 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.181020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.142663 restraints weight = 22430.898| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 2.04 r_work: 0.3525 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 19632 Z= 0.104 Angle : 0.510 10.512 26612 Z= 0.244 Chirality : 0.038 0.230 3020 Planarity : 0.003 0.040 3256 Dihedral : 8.183 79.001 2824 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.68 % Allowed : 20.66 % Favored : 76.67 % 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: 2.04 (0.18), residues: 2336 helix: 2.12 (0.14), residues: 1452 sheet: -0.29 (0.49), residues: 112 loop : 0.23 (0.23), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 333 HIS 0.003 0.001 HIS A 169 PHE 0.011 0.001 PHE C 547 TYR 0.039 0.001 TYR C 228 ARG 0.002 0.000 ARG D 459 Details of bonding type rmsd hydrogen bonds : bond 0.02970 ( 1068) hydrogen bonds : angle 3.29981 ( 3084) covalent geometry : bond 0.00238 (19632) covalent geometry : angle 0.50992 (26612) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11998.17 seconds wall clock time: 211 minutes 32.87 seconds (12692.87 seconds total)