Starting phenix.real_space_refine on Tue Jun 17 19:28:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t37_25650/06_2025/7t37_25650.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t37_25650/06_2025/7t37_25650.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t37_25650/06_2025/7t37_25650.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t37_25650/06_2025/7t37_25650.map" model { file = "/net/cci-nas-00/data/ceres_data/7t37_25650/06_2025/7t37_25650.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t37_25650/06_2025/7t37_25650.cif" } resolution = 3.7 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= 0.019 sd= 0.057 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: 5 Type Number sf(0) Gaussians S 116 5.16 5 B 4 2.79 5 C 13224 2.51 5 N 3388 2.21 5 O 3444 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 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: 20176 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 619, 5004 Classifications: {'peptide': 619} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 594} Chain breaks: 5 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 43 Chain: "B" Number of atoms: 5004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 619, 5004 Classifications: {'peptide': 619} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 594} Chain breaks: 5 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 43 Chain: "C" Number of atoms: 5004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 619, 5004 Classifications: {'peptide': 619} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 594} Chain breaks: 5 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 43 Chain: "D" Number of atoms: 5004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 619, 5004 Classifications: {'peptide': 619} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 594} Chain breaks: 5 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 43 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'FZ4': 1, 'P0T': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'FZ4': 1, 'P0T': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'FZ4': 1, 'P0T': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'FZ4': 1, 'P0T': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 12.37, per 1000 atoms: 0.61 Number of scatterers: 20176 At special positions: 0 Unit cell: (140.17, 140.17, 112.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 116 16.00 O 3444 8.00 N 3388 7.00 C 13224 6.00 B 4 5.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.45 Conformation dependent library (CDL) restraints added in 2.4 seconds 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4688 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 4 sheets defined 63.7% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.82 Creating SS restraints... Processing helix chain 'A' and resid 76 through 87 Processing helix chain 'A' and resid 89 through 93 removed outlier: 3.877A pdb=" N THR A 93 " --> pdb=" O GLU A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 103 Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 135 through 147 removed outlier: 3.624A pdb=" N GLY A 147 " --> pdb=" O ASP A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 174 removed outlier: 3.779A pdb=" N ILE A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 186 removed outlier: 3.547A pdb=" N ASN A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 200 Processing helix chain 'A' and resid 212 through 220 Processing helix chain 'A' and resid 222 through 231 removed outlier: 3.971A pdb=" N VAL A 226 " --> pdb=" O GLN A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 247 removed outlier: 4.067A pdb=" N ASN A 247 " --> pdb=" O SER A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 256 removed outlier: 3.623A pdb=" N VAL A 254 " --> pdb=" O LEU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 282 removed outlier: 3.659A pdb=" N ARG A 280 " --> pdb=" O GLN A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 290 removed outlier: 4.153A pdb=" N ILE A 290 " --> pdb=" O LEU A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 306 removed outlier: 3.667A pdb=" N GLY A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 316 removed outlier: 3.580A pdb=" N PHE A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 327 removed outlier: 3.568A pdb=" N LEU A 326 " --> pdb=" O TYR A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 362 Processing helix chain 'A' and resid 378 through 413 removed outlier: 3.532A pdb=" N ARG A 388 " --> pdb=" O GLU A 384 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N SER A 391 " --> pdb=" O ASP A 387 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N ARG A 392 " --> pdb=" O ARG A 388 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 459 Processing helix chain 'A' and resid 467 through 470 Processing helix chain 'A' and resid 471 through 492 removed outlier: 3.520A pdb=" N LEU A 475 " --> pdb=" O TYR A 471 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE A 476 " --> pdb=" O PHE A 472 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N LEU A 477 " --> pdb=" O GLU A 473 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N THR A 483 " --> pdb=" O GLN A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 512 removed outlier: 3.880A pdb=" N LEU A 500 " --> pdb=" O TRP A 496 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU A 501 " --> pdb=" O TYR A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 518 removed outlier: 4.078A pdb=" N GLY A 518 " --> pdb=" O TYR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 530 removed outlier: 3.774A pdb=" N TYR A 525 " --> pdb=" O HIS A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 559 removed outlier: 3.590A pdb=" N LEU A 537 " --> pdb=" O ILE A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 602 Processing helix chain 'A' and resid 618 through 650 removed outlier: 3.635A pdb=" N VAL A 635 " --> pdb=" O LEU A 631 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ASN A 650 " --> pdb=" O SER A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 672 removed outlier: 4.299A pdb=" N SER A 658 " --> pdb=" O ASP A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 719 removed outlier: 3.735A pdb=" N TRP A 715 " --> pdb=" O ASN A 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 87 Processing helix chain 'B' and resid 89 through 93 removed outlier: 3.874A pdb=" N THR B 93 " --> pdb=" O GLU B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 103 Processing helix chain 'B' and resid 119 through 127 Processing helix chain 'B' and resid 135 through 147 removed outlier: 3.618A pdb=" N GLY B 147 " --> pdb=" O ASP B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 174 removed outlier: 3.757A pdb=" N ILE B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 186 removed outlier: 3.544A pdb=" N ASN B 186 " --> pdb=" O LEU B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 200 Processing helix chain 'B' and resid 212 through 220 Processing helix chain 'B' and resid 222 through 231 removed outlier: 3.984A pdb=" N VAL B 226 " --> pdb=" O GLN B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 247 removed outlier: 4.066A pdb=" N ASN B 247 " --> pdb=" O SER B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 256 removed outlier: 3.911A pdb=" N VAL B 254 " --> pdb=" O LEU B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 282 removed outlier: 3.678A pdb=" N ARG B 280 " --> pdb=" O GLN B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 290 removed outlier: 4.164A pdb=" N ILE B 290 " --> pdb=" O LEU B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 306 removed outlier: 3.683A pdb=" N GLY B 306 " --> pdb=" O ALA B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 316 removed outlier: 3.670A pdb=" N PHE B 311 " --> pdb=" O LYS B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 327 removed outlier: 3.541A pdb=" N LEU B 326 " --> pdb=" O TYR B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 362 Processing helix chain 'B' and resid 378 through 413 removed outlier: 3.530A pdb=" N ARG B 388 " --> pdb=" O GLU B 384 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N SER B 391 " --> pdb=" O ASP B 387 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N ARG B 392 " --> pdb=" O ARG B 388 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE B 393 " --> pdb=" O LEU B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 459 Processing helix chain 'B' and resid 467 through 470 Processing helix chain 'B' and resid 471 through 492 removed outlier: 3.522A pdb=" N LEU B 475 " --> pdb=" O TYR B 471 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N PHE B 476 " --> pdb=" O PHE B 472 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N LEU B 477 " --> pdb=" O GLU B 473 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N THR B 483 " --> pdb=" O GLN B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 512 removed outlier: 3.874A pdb=" N LEU B 500 " --> pdb=" O TRP B 496 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU B 501 " --> pdb=" O TYR B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 518 removed outlier: 4.075A pdb=" N GLY B 518 " --> pdb=" O TYR B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 530 removed outlier: 3.788A pdb=" N TYR B 525 " --> pdb=" O HIS B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 559 removed outlier: 3.590A pdb=" N LEU B 537 " --> pdb=" O ILE B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 602 Processing helix chain 'B' and resid 618 through 650 removed outlier: 3.636A pdb=" N VAL B 635 " --> pdb=" O LEU B 631 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ASN B 650 " --> pdb=" O SER B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 672 removed outlier: 4.306A pdb=" N SER B 658 " --> pdb=" O ASP B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 719 removed outlier: 3.741A pdb=" N TRP B 715 " --> pdb=" O ASN B 711 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 87 Processing helix chain 'C' and resid 89 through 93 removed outlier: 3.873A pdb=" N THR C 93 " --> pdb=" O GLU C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 103 Processing helix chain 'C' and resid 119 through 127 Processing helix chain 'C' and resid 135 through 147 removed outlier: 3.624A pdb=" N GLY C 147 " --> pdb=" O ASP C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 174 removed outlier: 3.756A pdb=" N ILE C 170 " --> pdb=" O SER C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 186 removed outlier: 3.545A pdb=" N ASN C 186 " --> pdb=" O LEU C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 200 Processing helix chain 'C' and resid 212 through 220 Processing helix chain 'C' and resid 222 through 231 removed outlier: 3.965A pdb=" N VAL C 226 " --> pdb=" O GLN C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 247 removed outlier: 4.078A pdb=" N ASN C 247 " --> pdb=" O SER C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 256 removed outlier: 3.534A pdb=" N LEU C 253 " --> pdb=" O VAL C 249 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL C 254 " --> pdb=" O LEU C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 282 removed outlier: 3.683A pdb=" N ARG C 280 " --> pdb=" O GLN C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 290 removed outlier: 4.161A pdb=" N ILE C 290 " --> pdb=" O LEU C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 306 removed outlier: 3.666A pdb=" N GLY C 306 " --> pdb=" O ALA C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 316 removed outlier: 3.577A pdb=" N PHE C 311 " --> pdb=" O LYS C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 327 removed outlier: 3.560A pdb=" N LEU C 326 " --> pdb=" O TYR C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 362 Processing helix chain 'C' and resid 378 through 413 removed outlier: 3.530A pdb=" N ARG C 388 " --> pdb=" O GLU C 384 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N SER C 391 " --> pdb=" O ASP C 387 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N ARG C 392 " --> pdb=" O ARG C 388 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE C 393 " --> pdb=" O LEU C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 459 Processing helix chain 'C' and resid 467 through 470 Processing helix chain 'C' and resid 471 through 492 removed outlier: 3.540A pdb=" N LEU C 475 " --> pdb=" O TYR C 471 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE C 476 " --> pdb=" O PHE C 472 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N LEU C 477 " --> pdb=" O GLU C 473 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N THR C 483 " --> pdb=" O GLN C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 512 removed outlier: 3.871A pdb=" N LEU C 500 " --> pdb=" O TRP C 496 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU C 501 " --> pdb=" O TYR C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 518 removed outlier: 4.076A pdb=" N GLY C 518 " --> pdb=" O TYR C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 530 removed outlier: 3.787A pdb=" N TYR C 525 " --> pdb=" O HIS C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 559 removed outlier: 3.586A pdb=" N LEU C 537 " --> pdb=" O ILE C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 602 Processing helix chain 'C' and resid 618 through 650 removed outlier: 3.637A pdb=" N VAL C 635 " --> pdb=" O LEU C 631 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ASN C 650 " --> pdb=" O SER C 646 " (cutoff:3.500A) Processing helix chain 'C' and resid 654 through 672 removed outlier: 4.306A pdb=" N SER C 658 " --> pdb=" O ASP C 654 " (cutoff:3.500A) Processing helix chain 'C' and resid 711 through 719 removed outlier: 3.742A pdb=" N TRP C 715 " --> pdb=" O ASN C 711 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 87 Processing helix chain 'D' and resid 89 through 93 removed outlier: 3.864A pdb=" N THR D 93 " --> pdb=" O GLU D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 103 Processing helix chain 'D' and resid 119 through 127 Processing helix chain 'D' and resid 135 through 147 removed outlier: 3.628A pdb=" N GLY D 147 " --> pdb=" O ASP D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 174 removed outlier: 3.757A pdb=" N ILE D 170 " --> pdb=" O SER D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 186 removed outlier: 3.544A pdb=" N ASN D 186 " --> pdb=" O LEU D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 200 Processing helix chain 'D' and resid 212 through 220 Processing helix chain 'D' and resid 222 through 231 removed outlier: 3.964A pdb=" N VAL D 226 " --> pdb=" O GLN D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 247 removed outlier: 4.067A pdb=" N ASN D 247 " --> pdb=" O SER D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 256 removed outlier: 3.913A pdb=" N VAL D 254 " --> pdb=" O LEU D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 282 removed outlier: 3.683A pdb=" N ARG D 280 " --> pdb=" O GLN D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 290 removed outlier: 4.162A pdb=" N ILE D 290 " --> pdb=" O LEU D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 306 removed outlier: 3.673A pdb=" N GLY D 306 " --> pdb=" O ALA D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 316 removed outlier: 3.600A pdb=" N PHE D 311 " --> pdb=" O LYS D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 327 removed outlier: 3.556A pdb=" N LEU D 326 " --> pdb=" O TYR D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 362 Processing helix chain 'D' and resid 378 through 413 removed outlier: 3.530A pdb=" N ARG D 388 " --> pdb=" O GLU D 384 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N SER D 391 " --> pdb=" O ASP D 387 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N ARG D 392 " --> pdb=" O ARG D 388 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE D 393 " --> pdb=" O LEU D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 459 Processing helix chain 'D' and resid 467 through 470 Processing helix chain 'D' and resid 471 through 492 removed outlier: 3.539A pdb=" N LEU D 475 " --> pdb=" O TYR D 471 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE D 476 " --> pdb=" O PHE D 472 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N LEU D 477 " --> pdb=" O GLU D 473 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N THR D 483 " --> pdb=" O GLN D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 512 removed outlier: 3.872A pdb=" N LEU D 500 " --> pdb=" O TRP D 496 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU D 501 " --> pdb=" O TYR D 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 518 removed outlier: 4.055A pdb=" N GLY D 518 " --> pdb=" O TYR D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 530 removed outlier: 3.786A pdb=" N TYR D 525 " --> pdb=" O HIS D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 559 removed outlier: 3.589A pdb=" N LEU D 537 " --> pdb=" O ILE D 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 602 Processing helix chain 'D' and resid 618 through 650 removed outlier: 3.632A pdb=" N VAL D 635 " --> pdb=" O LEU D 631 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ASN D 650 " --> pdb=" O SER D 646 " (cutoff:3.500A) Processing helix chain 'D' and resid 654 through 672 removed outlier: 4.272A pdb=" N SER D 658 " --> pdb=" O ASP D 654 " (cutoff:3.500A) Processing helix chain 'D' and resid 711 through 719 removed outlier: 3.748A pdb=" N TRP D 715 " --> pdb=" O ASN D 711 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 330 through 335 removed outlier: 7.135A pdb=" N VAL A 340 " --> pdb=" O GLU A 332 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N CYS A 334 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL A 338 " --> pdb=" O CYS A 334 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 330 through 335 removed outlier: 7.135A pdb=" N VAL B 340 " --> pdb=" O GLU B 332 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N CYS B 334 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL B 338 " --> pdb=" O CYS B 334 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 330 through 335 removed outlier: 7.134A pdb=" N VAL C 340 " --> pdb=" O GLU C 332 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N CYS C 334 " --> pdb=" O VAL C 338 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL C 338 " --> pdb=" O CYS C 334 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 330 through 335 removed outlier: 7.107A pdb=" N VAL D 340 " --> pdb=" O GLU D 332 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N CYS D 334 " --> pdb=" O VAL D 338 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL D 338 " --> pdb=" O CYS D 334 " (cutoff:3.500A) 1059 hydrogen bonds defined for protein. 3045 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: 6.12 Time building geometry restraints manager: 5.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6264 1.34 - 1.46: 4694 1.46 - 1.58: 9546 1.58 - 1.70: 0 1.70 - 1.81: 180 Bond restraints: 20684 Sorted by residual: bond pdb=" C12 P0T D 802 " pdb=" O02 P0T D 802 " ideal model delta sigma weight residual 1.352 1.404 -0.052 2.00e-02 2.50e+03 6.80e+00 bond pdb=" C12 P0T A1001 " pdb=" O02 P0T A1001 " ideal model delta sigma weight residual 1.352 1.404 -0.052 2.00e-02 2.50e+03 6.71e+00 bond pdb=" C12 P0T C1001 " pdb=" O02 P0T C1001 " ideal model delta sigma weight residual 1.352 1.404 -0.052 2.00e-02 2.50e+03 6.71e+00 bond pdb=" C12 P0T B1001 " pdb=" O02 P0T B1001 " ideal model delta sigma weight residual 1.352 1.403 -0.051 2.00e-02 2.50e+03 6.57e+00 bond pdb=" C15 P0T B1001 " pdb=" C18 P0T B1001 " ideal model delta sigma weight residual 1.503 1.554 -0.051 2.00e-02 2.50e+03 6.47e+00 ... (remaining 20679 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 27185 2.19 - 4.38: 740 4.38 - 6.57: 74 6.57 - 8.76: 38 8.76 - 10.95: 7 Bond angle restraints: 28044 Sorted by residual: angle pdb=" CA VAL B 190 " pdb=" CB VAL B 190 " pdb=" CG1 VAL B 190 " ideal model delta sigma weight residual 110.40 117.27 -6.87 1.70e+00 3.46e-01 1.63e+01 angle pdb=" CA VAL A 190 " pdb=" CB VAL A 190 " pdb=" CG1 VAL A 190 " ideal model delta sigma weight residual 110.40 117.25 -6.85 1.70e+00 3.46e-01 1.62e+01 angle pdb=" CA VAL D 190 " pdb=" CB VAL D 190 " pdb=" CG1 VAL D 190 " ideal model delta sigma weight residual 110.40 117.21 -6.81 1.70e+00 3.46e-01 1.61e+01 angle pdb=" CA VAL C 190 " pdb=" CB VAL C 190 " pdb=" CG1 VAL C 190 " ideal model delta sigma weight residual 110.40 117.10 -6.70 1.70e+00 3.46e-01 1.56e+01 angle pdb=" CB MET C 404 " pdb=" CG MET C 404 " pdb=" SD MET C 404 " ideal model delta sigma weight residual 112.70 101.75 10.95 3.00e+00 1.11e-01 1.33e+01 ... (remaining 28039 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.02: 11310 19.02 - 38.04: 769 38.04 - 57.05: 97 57.05 - 76.07: 16 76.07 - 95.09: 12 Dihedral angle restraints: 12204 sinusoidal: 4964 harmonic: 7240 Sorted by residual: dihedral pdb=" CA ALA C 480 " pdb=" C ALA C 480 " pdb=" N LEU C 481 " pdb=" CA LEU C 481 " ideal model delta harmonic sigma weight residual -180.00 -160.82 -19.18 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA ALA D 480 " pdb=" C ALA D 480 " pdb=" N LEU D 481 " pdb=" CA LEU D 481 " ideal model delta harmonic sigma weight residual -180.00 -160.82 -19.18 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA ALA B 480 " pdb=" C ALA B 480 " pdb=" N LEU B 481 " pdb=" CA LEU B 481 " ideal model delta harmonic sigma weight residual -180.00 -160.91 -19.09 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 12201 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2013 0.040 - 0.080: 871 0.080 - 0.120: 213 0.120 - 0.159: 39 0.159 - 0.199: 8 Chirality restraints: 3144 Sorted by residual: chirality pdb=" CB VAL B 190 " pdb=" CA VAL B 190 " pdb=" CG1 VAL B 190 " pdb=" CG2 VAL B 190 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.93e-01 chirality pdb=" CB VAL D 190 " pdb=" CA VAL D 190 " pdb=" CG1 VAL D 190 " pdb=" CG2 VAL D 190 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.19 2.00e-01 2.50e+01 9.43e-01 chirality pdb=" CB VAL C 190 " pdb=" CA VAL C 190 " pdb=" CG1 VAL C 190 " pdb=" CG2 VAL C 190 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.40e-01 ... (remaining 3141 not shown) Planarity restraints: 3460 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL D 484 " -0.012 2.00e-02 2.50e+03 2.41e-02 5.83e+00 pdb=" C VAL D 484 " 0.042 2.00e-02 2.50e+03 pdb=" O VAL D 484 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU D 485 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 484 " 0.012 2.00e-02 2.50e+03 2.41e-02 5.81e+00 pdb=" C VAL B 484 " -0.042 2.00e-02 2.50e+03 pdb=" O VAL B 484 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU B 485 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 484 " 0.012 2.00e-02 2.50e+03 2.38e-02 5.65e+00 pdb=" C VAL A 484 " -0.041 2.00e-02 2.50e+03 pdb=" O VAL A 484 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU A 485 " 0.014 2.00e-02 2.50e+03 ... (remaining 3457 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4477 2.78 - 3.31: 18265 3.31 - 3.84: 31943 3.84 - 4.37: 35471 4.37 - 4.90: 63596 Nonbonded interactions: 153752 Sorted by model distance: nonbonded pdb=" OH TYR A 455 " pdb=" OE1 GLU A 473 " model vdw 2.247 3.040 nonbonded pdb=" NH2 ARG C 706 " pdb=" OE1 GLN D 40 " model vdw 2.323 3.120 nonbonded pdb=" NH2 ARG B 706 " pdb=" OE1 GLN C 40 " model vdw 2.324 3.120 nonbonded pdb=" NH2 ARG A 706 " pdb=" OE1 GLN B 40 " model vdw 2.325 3.120 nonbonded pdb=" OE1 GLN A 40 " pdb=" NH2 ARG D 706 " model vdw 2.329 3.120 ... (remaining 153747 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' and resid 31 through 720) selection = (chain 'B' and resid 31 through 720) selection = (chain 'C' and resid 31 through 720) selection = (chain 'D' and resid 31 through 720) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.770 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 44.270 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 20684 Z= 0.279 Angle : 0.847 10.948 28044 Z= 0.429 Chirality : 0.046 0.199 3144 Planarity : 0.006 0.051 3460 Dihedral : 13.204 95.088 7516 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.43 (0.15), residues: 2428 helix: -0.34 (0.13), residues: 1420 sheet: -0.34 (0.66), residues: 68 loop : -1.86 (0.18), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 333 HIS 0.007 0.002 HIS D 651 PHE 0.020 0.003 PHE C 394 TYR 0.027 0.002 TYR B 335 ARG 0.003 0.001 ARG A 706 Details of bonding type rmsd hydrogen bonds : bond 0.15885 ( 1059) hydrogen bonds : angle 5.21364 ( 3045) covalent geometry : bond 0.00651 (20684) covalent geometry : angle 0.84720 (28044) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 2.166 Fit side-chains REVERT: A 42 GLU cc_start: 0.7136 (mm-30) cc_final: 0.6800 (mm-30) REVERT: A 529 ILE cc_start: 0.9180 (tp) cc_final: 0.8947 (tp) REVERT: B 42 GLU cc_start: 0.7143 (mm-30) cc_final: 0.6794 (mm-30) REVERT: B 529 ILE cc_start: 0.9184 (tp) cc_final: 0.8948 (tp) REVERT: C 42 GLU cc_start: 0.7144 (mm-30) cc_final: 0.6825 (mm-30) REVERT: C 529 ILE cc_start: 0.9195 (tp) cc_final: 0.8957 (tp) REVERT: D 42 GLU cc_start: 0.7164 (mm-30) cc_final: 0.6839 (mm-30) REVERT: D 529 ILE cc_start: 0.9181 (tp) cc_final: 0.8949 (tp) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.2752 time to fit residues: 78.7978 Evaluate side-chains 141 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 2.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 3.9990 chunk 184 optimal weight: 0.4980 chunk 102 optimal weight: 7.9990 chunk 63 optimal weight: 9.9990 chunk 124 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 chunk 191 optimal weight: 2.9990 chunk 74 optimal weight: 9.9990 chunk 116 optimal weight: 7.9990 chunk 142 optimal weight: 6.9990 chunk 221 optimal weight: 0.9980 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 HIS B 370 HIS C 370 HIS D 370 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.105093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.083893 restraints weight = 39315.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.086652 restraints weight = 23035.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.088483 restraints weight = 16266.840| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 20684 Z= 0.209 Angle : 0.595 6.917 28044 Z= 0.297 Chirality : 0.038 0.123 3144 Planarity : 0.004 0.037 3460 Dihedral : 6.553 78.089 2812 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.74 % Allowed : 6.39 % Favored : 92.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.02 (0.17), residues: 2428 helix: 0.86 (0.14), residues: 1428 sheet: 0.11 (0.69), residues: 68 loop : -1.38 (0.19), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 333 HIS 0.006 0.002 HIS B 313 PHE 0.011 0.002 PHE B 540 TYR 0.015 0.002 TYR A 98 ARG 0.002 0.000 ARG A 369 Details of bonding type rmsd hydrogen bonds : bond 0.04138 ( 1059) hydrogen bonds : angle 3.49695 ( 3045) covalent geometry : bond 0.00505 (20684) covalent geometry : angle 0.59467 (28044) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 153 time to evaluate : 2.120 Fit side-chains REVERT: A 42 GLU cc_start: 0.7151 (mm-30) cc_final: 0.6917 (mm-30) REVERT: A 503 LEU cc_start: 0.8080 (tp) cc_final: 0.7855 (tt) REVERT: A 529 ILE cc_start: 0.9075 (tp) cc_final: 0.8709 (tp) REVERT: B 42 GLU cc_start: 0.7137 (mm-30) cc_final: 0.6907 (mm-30) REVERT: B 503 LEU cc_start: 0.8116 (tp) cc_final: 0.7863 (tt) REVERT: B 529 ILE cc_start: 0.9072 (tp) cc_final: 0.8708 (tp) REVERT: C 42 GLU cc_start: 0.7137 (mm-30) cc_final: 0.6915 (mm-30) REVERT: C 503 LEU cc_start: 0.8086 (tp) cc_final: 0.7826 (tt) REVERT: C 529 ILE cc_start: 0.9096 (tp) cc_final: 0.8737 (tp) REVERT: D 42 GLU cc_start: 0.7146 (mm-30) cc_final: 0.6919 (mm-30) REVERT: D 503 LEU cc_start: 0.8077 (tp) cc_final: 0.7820 (tt) REVERT: D 529 ILE cc_start: 0.9070 (tp) cc_final: 0.8705 (tp) outliers start: 16 outliers final: 12 residues processed: 161 average time/residue: 0.2505 time to fit residues: 68.3598 Evaluate side-chains 165 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 153 time to evaluate : 2.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 483 THR Chi-restraints excluded: chain D residue 648 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 33 optimal weight: 4.9990 chunk 227 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 179 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 chunk 103 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 130 optimal weight: 9.9990 chunk 187 optimal weight: 8.9990 chunk 240 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 = 0.3402 r_free = 0.3402 target = 0.104129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.082756 restraints weight = 39143.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.085535 restraints weight = 22539.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.087393 restraints weight = 15885.660| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 20684 Z= 0.198 Angle : 0.564 6.451 28044 Z= 0.280 Chirality : 0.037 0.126 3144 Planarity : 0.003 0.035 3460 Dihedral : 6.274 78.257 2812 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.88 % Allowed : 9.72 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.40 (0.17), residues: 2428 helix: 1.28 (0.14), residues: 1428 sheet: 0.07 (0.68), residues: 68 loop : -1.34 (0.19), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 333 HIS 0.004 0.001 HIS D 313 PHE 0.009 0.002 PHE C 612 TYR 0.018 0.002 TYR A 98 ARG 0.003 0.000 ARG A 706 Details of bonding type rmsd hydrogen bonds : bond 0.03952 ( 1059) hydrogen bonds : angle 3.37707 ( 3045) covalent geometry : bond 0.00480 (20684) covalent geometry : angle 0.56356 (28044) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 152 time to evaluate : 2.213 Fit side-chains REVERT: A 42 GLU cc_start: 0.7290 (mm-30) cc_final: 0.6985 (mm-30) REVERT: A 105 TYR cc_start: 0.7694 (m-80) cc_final: 0.7478 (m-80) REVERT: A 494 THR cc_start: 0.8926 (t) cc_final: 0.8659 (t) REVERT: B 42 GLU cc_start: 0.7303 (mm-30) cc_final: 0.6998 (mm-30) REVERT: B 105 TYR cc_start: 0.7710 (m-80) cc_final: 0.7503 (m-80) REVERT: B 494 THR cc_start: 0.8926 (t) cc_final: 0.8673 (t) REVERT: C 42 GLU cc_start: 0.7299 (mm-30) cc_final: 0.6999 (mm-30) REVERT: C 494 THR cc_start: 0.8929 (t) cc_final: 0.8668 (t) REVERT: D 42 GLU cc_start: 0.7290 (mm-30) cc_final: 0.7011 (mm-30) REVERT: D 494 THR cc_start: 0.8903 (t) cc_final: 0.8634 (t) outliers start: 19 outliers final: 12 residues processed: 167 average time/residue: 0.2566 time to fit residues: 72.4513 Evaluate side-chains 161 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 149 time to evaluate : 2.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 483 THR Chi-restraints excluded: chain D residue 648 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 44 optimal weight: 0.7980 chunk 213 optimal weight: 2.9990 chunk 79 optimal weight: 9.9990 chunk 62 optimal weight: 20.0000 chunk 96 optimal weight: 2.9990 chunk 164 optimal weight: 0.2980 chunk 25 optimal weight: 0.9990 chunk 212 optimal weight: 3.9990 chunk 100 optimal weight: 0.3980 chunk 137 optimal weight: 4.9990 chunk 243 optimal weight: 0.9980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 487 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.109016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.087803 restraints weight = 38659.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.090714 restraints weight = 21900.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.092701 restraints weight = 15248.320| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 20684 Z= 0.086 Angle : 0.443 6.463 28044 Z= 0.220 Chirality : 0.034 0.113 3144 Planarity : 0.003 0.033 3460 Dihedral : 5.775 76.621 2812 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.79 % Allowed : 11.06 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.02 (0.17), residues: 2428 helix: 1.85 (0.14), residues: 1436 sheet: -0.03 (0.64), residues: 68 loop : -1.19 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 509 HIS 0.003 0.001 HIS D 651 PHE 0.007 0.001 PHE A 476 TYR 0.018 0.001 TYR A 98 ARG 0.001 0.000 ARG B 706 Details of bonding type rmsd hydrogen bonds : bond 0.02802 ( 1059) hydrogen bonds : angle 2.98833 ( 3045) covalent geometry : bond 0.00198 (20684) covalent geometry : angle 0.44299 (28044) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 158 time to evaluate : 2.210 Fit side-chains REVERT: A 42 GLU cc_start: 0.7365 (mm-30) cc_final: 0.7127 (mm-30) REVERT: A 494 THR cc_start: 0.8843 (t) cc_final: 0.8599 (t) REVERT: B 42 GLU cc_start: 0.7384 (mm-30) cc_final: 0.7143 (mm-30) REVERT: B 494 THR cc_start: 0.8864 (t) cc_final: 0.8605 (t) REVERT: C 42 GLU cc_start: 0.7371 (mm-30) cc_final: 0.7145 (mm-30) REVERT: C 494 THR cc_start: 0.8838 (t) cc_final: 0.8593 (t) REVERT: D 42 GLU cc_start: 0.7387 (mm-30) cc_final: 0.7151 (mm-30) REVERT: D 494 THR cc_start: 0.8847 (t) cc_final: 0.8591 (t) outliers start: 17 outliers final: 16 residues processed: 171 average time/residue: 0.2531 time to fit residues: 73.4083 Evaluate side-chains 170 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 154 time to evaluate : 2.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain D residue 485 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 44 optimal weight: 5.9990 chunk 241 optimal weight: 10.0000 chunk 240 optimal weight: 1.9990 chunk 157 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 chunk 67 optimal weight: 10.0000 chunk 79 optimal weight: 8.9990 chunk 202 optimal weight: 0.0970 chunk 129 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 overall best weight: 3.4186 ------------------------------------------------------------------------------- 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 = 0.3398 r_free = 0.3398 target = 0.103775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.082298 restraints weight = 39644.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.085070 restraints weight = 22858.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.086943 restraints weight = 16151.108| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 20684 Z= 0.219 Angle : 0.572 6.956 28044 Z= 0.281 Chirality : 0.038 0.129 3144 Planarity : 0.003 0.033 3460 Dihedral : 6.119 77.941 2812 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.30 % Allowed : 12.27 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.90 (0.18), residues: 2428 helix: 1.72 (0.14), residues: 1428 sheet: -0.83 (0.56), residues: 88 loop : -1.10 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 333 HIS 0.005 0.001 HIS C 169 PHE 0.011 0.002 PHE D 519 TYR 0.017 0.002 TYR A 98 ARG 0.003 0.000 ARG D 706 Details of bonding type rmsd hydrogen bonds : bond 0.03836 ( 1059) hydrogen bonds : angle 3.27573 ( 3045) covalent geometry : bond 0.00531 (20684) covalent geometry : angle 0.57221 (28044) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 2.322 Fit side-chains REVERT: A 42 GLU cc_start: 0.7496 (mm-30) cc_final: 0.7104 (mm-30) REVERT: A 494 THR cc_start: 0.8932 (t) cc_final: 0.8654 (t) REVERT: B 42 GLU cc_start: 0.7439 (mm-30) cc_final: 0.7079 (mm-30) REVERT: B 494 THR cc_start: 0.8950 (t) cc_final: 0.8668 (t) REVERT: C 42 GLU cc_start: 0.7554 (mm-30) cc_final: 0.7170 (mm-30) REVERT: C 494 THR cc_start: 0.8929 (t) cc_final: 0.8651 (t) REVERT: D 42 GLU cc_start: 0.7496 (mm-30) cc_final: 0.7115 (mm-30) REVERT: D 494 THR cc_start: 0.8949 (t) cc_final: 0.8667 (t) outliers start: 28 outliers final: 27 residues processed: 175 average time/residue: 0.2631 time to fit residues: 77.7749 Evaluate side-chains 175 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 148 time to evaluate : 2.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain D residue 483 THR Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 533 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 6 optimal weight: 8.9990 chunk 161 optimal weight: 0.7980 chunk 169 optimal weight: 3.9990 chunk 191 optimal weight: 3.9990 chunk 238 optimal weight: 20.0000 chunk 118 optimal weight: 6.9990 chunk 141 optimal weight: 2.9990 chunk 177 optimal weight: 9.9990 chunk 77 optimal weight: 7.9990 chunk 24 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 651 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.105822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.084371 restraints weight = 38933.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.087219 restraints weight = 22180.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.089081 restraints weight = 15537.000| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20684 Z= 0.133 Angle : 0.487 7.119 28044 Z= 0.242 Chirality : 0.036 0.120 3144 Planarity : 0.003 0.032 3460 Dihedral : 5.910 76.412 2812 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.48 % Allowed : 12.73 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.15 (0.17), residues: 2428 helix: 1.96 (0.14), residues: 1428 sheet: -0.18 (0.63), residues: 68 loop : -1.11 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 333 HIS 0.003 0.001 HIS D 313 PHE 0.009 0.001 PHE D 519 TYR 0.018 0.001 TYR C 98 ARG 0.002 0.000 ARG C 706 Details of bonding type rmsd hydrogen bonds : bond 0.03252 ( 1059) hydrogen bonds : angle 3.08142 ( 3045) covalent geometry : bond 0.00323 (20684) covalent geometry : angle 0.48676 (28044) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 155 time to evaluate : 2.182 Fit side-chains REVERT: A 42 GLU cc_start: 0.7477 (mm-30) cc_final: 0.7187 (mm-30) REVERT: A 494 THR cc_start: 0.8865 (t) cc_final: 0.8597 (t) REVERT: B 42 GLU cc_start: 0.7486 (mm-30) cc_final: 0.7199 (mm-30) REVERT: B 494 THR cc_start: 0.8882 (t) cc_final: 0.8609 (t) REVERT: C 42 GLU cc_start: 0.7493 (mm-30) cc_final: 0.7192 (mm-30) REVERT: C 494 THR cc_start: 0.8863 (t) cc_final: 0.8594 (t) REVERT: D 42 GLU cc_start: 0.7574 (mm-30) cc_final: 0.7234 (mm-30) REVERT: D 494 THR cc_start: 0.8880 (t) cc_final: 0.8609 (t) outliers start: 32 outliers final: 31 residues processed: 183 average time/residue: 0.2525 time to fit residues: 78.5933 Evaluate side-chains 182 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 151 time to evaluate : 2.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain D residue 483 THR Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 710 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 55 optimal weight: 20.0000 chunk 22 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 79 optimal weight: 0.2980 chunk 149 optimal weight: 0.7980 chunk 90 optimal weight: 7.9990 chunk 230 optimal weight: 3.9990 chunk 36 optimal weight: 20.0000 chunk 24 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 GLN B 487 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.109011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.087913 restraints weight = 38318.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.090825 restraints weight = 21705.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.092780 restraints weight = 15147.192| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20684 Z= 0.085 Angle : 0.432 6.275 28044 Z= 0.216 Chirality : 0.034 0.114 3144 Planarity : 0.003 0.032 3460 Dihedral : 5.508 74.509 2812 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.39 % Allowed : 12.87 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.55 (0.18), residues: 2428 helix: 2.32 (0.14), residues: 1436 sheet: -0.08 (0.62), residues: 68 loop : -1.05 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP C 509 HIS 0.002 0.001 HIS C 370 PHE 0.009 0.001 PHE B 519 TYR 0.020 0.001 TYR D 98 ARG 0.002 0.000 ARG B 706 Details of bonding type rmsd hydrogen bonds : bond 0.02684 ( 1059) hydrogen bonds : angle 2.87863 ( 3045) covalent geometry : bond 0.00194 (20684) covalent geometry : angle 0.43242 (28044) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 157 time to evaluate : 2.169 Fit side-chains REVERT: A 42 GLU cc_start: 0.7492 (mm-30) cc_final: 0.7232 (mm-30) REVERT: A 494 THR cc_start: 0.8824 (t) cc_final: 0.8587 (t) REVERT: B 42 GLU cc_start: 0.7511 (mm-30) cc_final: 0.7243 (mm-30) REVERT: B 494 THR cc_start: 0.8832 (t) cc_final: 0.8591 (t) REVERT: B 528 MET cc_start: 0.7364 (ttm) cc_final: 0.7161 (mtt) REVERT: C 42 GLU cc_start: 0.7507 (mm-30) cc_final: 0.7262 (mm-30) REVERT: C 494 THR cc_start: 0.8826 (t) cc_final: 0.8587 (t) REVERT: C 528 MET cc_start: 0.7362 (ttm) cc_final: 0.7160 (mtt) REVERT: D 42 GLU cc_start: 0.7496 (mm-30) cc_final: 0.7251 (mm-30) REVERT: D 494 THR cc_start: 0.8830 (t) cc_final: 0.8589 (t) REVERT: D 662 LEU cc_start: 0.8410 (tp) cc_final: 0.8204 (tp) outliers start: 30 outliers final: 20 residues processed: 186 average time/residue: 0.2517 time to fit residues: 79.8711 Evaluate side-chains 176 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 156 time to evaluate : 2.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 710 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 37 optimal weight: 6.9990 chunk 167 optimal weight: 0.2980 chunk 213 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 185 optimal weight: 9.9990 chunk 196 optimal weight: 8.9990 chunk 163 optimal weight: 7.9990 chunk 140 optimal weight: 0.5980 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 = 0.3428 r_free = 0.3428 target = 0.105790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.084520 restraints weight = 39166.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.087364 restraints weight = 22309.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.089285 restraints weight = 15622.659| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 20684 Z= 0.148 Angle : 0.499 7.562 28044 Z= 0.245 Chirality : 0.036 0.122 3144 Planarity : 0.003 0.032 3460 Dihedral : 5.655 75.086 2812 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.53 % Allowed : 13.24 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.18), residues: 2428 helix: 2.28 (0.14), residues: 1432 sheet: -0.09 (0.62), residues: 68 loop : -1.00 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 333 HIS 0.003 0.001 HIS D 313 PHE 0.011 0.001 PHE A 519 TYR 0.017 0.001 TYR D 98 ARG 0.002 0.000 ARG B 706 Details of bonding type rmsd hydrogen bonds : bond 0.03246 ( 1059) hydrogen bonds : angle 3.00806 ( 3045) covalent geometry : bond 0.00359 (20684) covalent geometry : angle 0.49862 (28044) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 149 time to evaluate : 2.108 Fit side-chains REVERT: A 42 GLU cc_start: 0.7493 (mm-30) cc_final: 0.7162 (mm-30) REVERT: A 494 THR cc_start: 0.8865 (t) cc_final: 0.8600 (t) REVERT: B 42 GLU cc_start: 0.7521 (mm-30) cc_final: 0.7176 (mm-30) REVERT: B 494 THR cc_start: 0.8865 (t) cc_final: 0.8598 (t) REVERT: C 42 GLU cc_start: 0.7512 (mm-30) cc_final: 0.7174 (mm-30) REVERT: C 494 THR cc_start: 0.8864 (t) cc_final: 0.8596 (t) REVERT: D 42 GLU cc_start: 0.7499 (mm-30) cc_final: 0.7159 (mm-30) REVERT: D 494 THR cc_start: 0.8868 (t) cc_final: 0.8600 (t) outliers start: 33 outliers final: 32 residues processed: 177 average time/residue: 0.2470 time to fit residues: 74.3438 Evaluate side-chains 181 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 149 time to evaluate : 2.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain D residue 483 THR Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 710 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 77 optimal weight: 6.9990 chunk 226 optimal weight: 1.9990 chunk 145 optimal weight: 0.9990 chunk 133 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 201 optimal weight: 1.9990 chunk 241 optimal weight: 10.0000 chunk 165 optimal weight: 7.9990 chunk 187 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 = 0.3454 r_free = 0.3454 target = 0.107520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.086457 restraints weight = 38688.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.089295 restraints weight = 22093.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.091210 restraints weight = 15493.765| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 20684 Z= 0.104 Angle : 0.464 8.422 28044 Z= 0.227 Chirality : 0.035 0.115 3144 Planarity : 0.003 0.032 3460 Dihedral : 5.490 73.954 2812 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.34 % Allowed : 13.66 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.18), residues: 2428 helix: 2.38 (0.14), residues: 1436 sheet: -0.14 (0.60), residues: 68 loop : -0.94 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 333 HIS 0.002 0.001 HIS D 313 PHE 0.009 0.001 PHE B 519 TYR 0.020 0.001 TYR D 98 ARG 0.003 0.000 ARG B 706 Details of bonding type rmsd hydrogen bonds : bond 0.02916 ( 1059) hydrogen bonds : angle 2.92293 ( 3045) covalent geometry : bond 0.00247 (20684) covalent geometry : angle 0.46434 (28044) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 157 time to evaluate : 2.320 Fit side-chains REVERT: A 42 GLU cc_start: 0.7465 (mm-30) cc_final: 0.7178 (mm-30) REVERT: A 494 THR cc_start: 0.8845 (t) cc_final: 0.8592 (t) REVERT: B 42 GLU cc_start: 0.7502 (mm-30) cc_final: 0.7190 (mm-30) REVERT: B 494 THR cc_start: 0.8849 (t) cc_final: 0.8621 (t) REVERT: B 528 MET cc_start: 0.7398 (ttm) cc_final: 0.7185 (mtt) REVERT: C 42 GLU cc_start: 0.7516 (mm-30) cc_final: 0.7196 (mm-30) REVERT: C 494 THR cc_start: 0.8848 (t) cc_final: 0.8593 (t) REVERT: C 528 MET cc_start: 0.7397 (ttm) cc_final: 0.7184 (mtt) REVERT: D 42 GLU cc_start: 0.7498 (mm-30) cc_final: 0.7188 (mm-30) REVERT: D 494 THR cc_start: 0.8851 (t) cc_final: 0.8584 (t) REVERT: D 651 HIS cc_start: 0.7044 (OUTLIER) cc_final: 0.6804 (m-70) outliers start: 29 outliers final: 28 residues processed: 181 average time/residue: 0.2608 time to fit residues: 80.2030 Evaluate side-chains 184 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 155 time to evaluate : 2.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 651 HIS Chi-restraints excluded: chain D residue 710 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 134 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 chunk 201 optimal weight: 5.9990 chunk 42 optimal weight: 0.0980 chunk 15 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 chunk 215 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 222 optimal weight: 3.9990 chunk 73 optimal weight: 0.0270 overall best weight: 1.5842 ------------------------------------------------------------------------------- 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 = 0.3443 r_free = 0.3443 target = 0.106743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.085735 restraints weight = 38853.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.088548 restraints weight = 22167.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.090444 restraints weight = 15528.052| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20684 Z= 0.120 Angle : 0.484 7.995 28044 Z= 0.236 Chirality : 0.035 0.119 3144 Planarity : 0.003 0.032 3460 Dihedral : 5.494 73.649 2812 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.34 % Allowed : 13.98 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.65 (0.18), residues: 2428 helix: 2.36 (0.14), residues: 1436 sheet: -0.11 (0.61), residues: 68 loop : -0.91 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 333 HIS 0.003 0.001 HIS D 313 PHE 0.010 0.001 PHE A 519 TYR 0.019 0.001 TYR C 98 ARG 0.002 0.000 ARG B 706 Details of bonding type rmsd hydrogen bonds : bond 0.03059 ( 1059) hydrogen bonds : angle 2.95844 ( 3045) covalent geometry : bond 0.00289 (20684) covalent geometry : angle 0.48390 (28044) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 153 time to evaluate : 2.568 Fit side-chains revert: symmetry clash REVERT: A 42 GLU cc_start: 0.7475 (mm-30) cc_final: 0.7163 (mm-30) REVERT: A 491 PHE cc_start: 0.7319 (m-80) cc_final: 0.6870 (m-10) REVERT: A 494 THR cc_start: 0.8845 (t) cc_final: 0.8607 (t) REVERT: B 42 GLU cc_start: 0.7504 (mm-30) cc_final: 0.7183 (mm-30) REVERT: B 491 PHE cc_start: 0.7334 (m-80) cc_final: 0.6885 (m-10) REVERT: B 494 THR cc_start: 0.8856 (t) cc_final: 0.8594 (t) REVERT: C 42 GLU cc_start: 0.7505 (mm-30) cc_final: 0.7180 (mm-30) REVERT: C 491 PHE cc_start: 0.7312 (m-80) cc_final: 0.6864 (m-10) REVERT: C 494 THR cc_start: 0.8844 (t) cc_final: 0.8609 (t) REVERT: D 42 GLU cc_start: 0.7496 (mm-30) cc_final: 0.7184 (mm-30) REVERT: D 491 PHE cc_start: 0.7313 (m-80) cc_final: 0.6865 (m-10) REVERT: D 494 THR cc_start: 0.8848 (t) cc_final: 0.8610 (t) REVERT: D 651 HIS cc_start: 0.7032 (OUTLIER) cc_final: 0.6791 (m-70) outliers start: 29 outliers final: 28 residues processed: 177 average time/residue: 0.2638 time to fit residues: 79.8636 Evaluate side-chains 181 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 152 time to evaluate : 2.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 651 HIS Chi-restraints excluded: chain D residue 710 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 173 optimal weight: 8.9990 chunk 105 optimal weight: 0.9990 chunk 186 optimal weight: 0.0570 chunk 189 optimal weight: 10.0000 chunk 133 optimal weight: 0.9980 chunk 41 optimal weight: 7.9990 chunk 166 optimal weight: 0.5980 chunk 202 optimal weight: 3.9990 chunk 221 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 181 optimal weight: 10.0000 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 487 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.109425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.088578 restraints weight = 38270.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.091528 restraints weight = 21130.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.093516 restraints weight = 14495.742| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20684 Z= 0.083 Angle : 0.444 6.934 28044 Z= 0.217 Chirality : 0.034 0.113 3144 Planarity : 0.003 0.032 3460 Dihedral : 5.205 71.670 2812 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.34 % Allowed : 14.07 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.86 (0.18), residues: 2428 helix: 2.57 (0.14), residues: 1436 sheet: -0.03 (0.60), residues: 68 loop : -0.89 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP B 509 HIS 0.002 0.001 HIS C 370 PHE 0.007 0.001 PHE C 209 TYR 0.020 0.001 TYR D 98 ARG 0.002 0.000 ARG B 706 Details of bonding type rmsd hydrogen bonds : bond 0.02626 ( 1059) hydrogen bonds : angle 2.83664 ( 3045) covalent geometry : bond 0.00190 (20684) covalent geometry : angle 0.44418 (28044) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4894.92 seconds wall clock time: 86 minutes 29.25 seconds (5189.25 seconds total)