Starting phenix.real_space_refine on Tue Jun 17 03:13:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t6l_25718/06_2025/7t6l_25718.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t6l_25718/06_2025/7t6l_25718.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/7t6l_25718/06_2025/7t6l_25718.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t6l_25718/06_2025/7t6l_25718.map" model { file = "/net/cci-nas-00/data/ceres_data/7t6l_25718/06_2025/7t6l_25718.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t6l_25718/06_2025/7t6l_25718.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= 0.002 sd= 0.020 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: 4 Type Number sf(0) Gaussians S 140 5.16 5 C 12548 2.51 5 N 3284 2.21 5 O 3440 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 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: 19412 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Chain: "B" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Chain: "C" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Chain: "D" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Time building chain proxies: 13.41, per 1000 atoms: 0.69 Number of scatterers: 19412 At special positions: 0 Unit cell: (141.93, 141.93, 121.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 140 16.00 O 3440 8.00 N 3284 7.00 C 12548 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.34 Conformation dependent library (CDL) restraints added in 2.5 seconds 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4576 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 8 sheets defined 64.7% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.67 Creating SS restraints... Processing helix chain 'A' and resid 29 through 47 removed outlier: 3.720A pdb=" N SER A 47 " --> pdb=" O ARG A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 56 removed outlier: 3.587A pdb=" N GLN A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN A 56 " --> pdb=" O ALA A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 67 removed outlier: 3.679A pdb=" N ASN A 67 " --> pdb=" O ILE A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 removed outlier: 3.731A pdb=" N TYR A 89 " --> pdb=" O VAL A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 102 removed outlier: 3.610A pdb=" N ALA A 95 " --> pdb=" O ASN A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 107 removed outlier: 3.989A pdb=" N ALA A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.737A pdb=" N ILE A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 140 Processing helix chain 'A' and resid 165 through 174 Processing helix chain 'A' and resid 175 through 184 Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 213 through 222 Processing helix chain 'A' and resid 242 through 250 Processing helix chain 'A' and resid 252 through 264 removed outlier: 4.078A pdb=" N LYS A 262 " --> pdb=" O HIS A 258 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG A 263 " --> pdb=" O LEU A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 298 Processing helix chain 'A' and resid 303 through 308 removed outlier: 3.895A pdb=" N ILE A 307 " --> pdb=" O GLU A 303 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 303 through 308' Processing helix chain 'A' and resid 310 through 324 removed outlier: 3.918A pdb=" N GLU A 315 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LEU A 316 " --> pdb=" O PRO A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 349 Processing helix chain 'A' and resid 379 through 410 removed outlier: 3.629A pdb=" N GLY A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) Proline residue: A 405 - end of helix Processing helix chain 'A' and resid 411 through 418 removed outlier: 3.640A pdb=" N GLN A 418 " --> pdb=" O ARG A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 445 Processing helix chain 'A' and resid 450 through 464 removed outlier: 3.942A pdb=" N PHE A 456 " --> pdb=" O VAL A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 470 removed outlier: 4.098A pdb=" N ARG A 470 " --> pdb=" O TYR A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 513 removed outlier: 3.641A pdb=" N LEU A 490 " --> pdb=" O ILE A 486 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N MET A 491 " --> pdb=" O PHE A 487 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ARG A 492 " --> pdb=" O GLY A 488 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE A 493 " --> pdb=" O ASP A 489 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL A 499 " --> pdb=" O TRP A 495 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLY A 503 " --> pdb=" O VAL A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 538 removed outlier: 3.518A pdb=" N LEU A 538 " --> pdb=" O PHE A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 566 removed outlier: 3.725A pdb=" N CYS A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE A 557 " --> pdb=" O PHE A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 605 removed outlier: 3.940A pdb=" N ASN A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N GLN A 587 " --> pdb=" O TRP A 583 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N GLU A 588 " --> pdb=" O ARG A 584 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLU A 591 " --> pdb=" O GLN A 587 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL A 598 " --> pdb=" O ARG A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 613 Processing helix chain 'B' and resid 30 through 47 removed outlier: 3.717A pdb=" N SER B 47 " --> pdb=" O ARG B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 56 removed outlier: 3.586A pdb=" N GLN B 51 " --> pdb=" O SER B 47 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN B 56 " --> pdb=" O ALA B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 67 removed outlier: 3.679A pdb=" N ASN B 67 " --> pdb=" O ILE B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 removed outlier: 3.735A pdb=" N TYR B 89 " --> pdb=" O VAL B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 102 removed outlier: 3.612A pdb=" N ALA B 95 " --> pdb=" O ASN B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 107 removed outlier: 3.991A pdb=" N ALA B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.733A pdb=" N ILE B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 140 Processing helix chain 'B' and resid 165 through 174 Processing helix chain 'B' and resid 175 through 184 Processing helix chain 'B' and resid 198 through 205 Processing helix chain 'B' and resid 213 through 222 Processing helix chain 'B' and resid 242 through 251 removed outlier: 3.708A pdb=" N GLY B 251 " --> pdb=" O ALA B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 264 removed outlier: 4.078A pdb=" N LYS B 262 " --> pdb=" O HIS B 258 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG B 263 " --> pdb=" O LEU B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 298 Processing helix chain 'B' and resid 303 through 308 removed outlier: 3.857A pdb=" N ILE B 307 " --> pdb=" O GLU B 303 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 303 through 308' Processing helix chain 'B' and resid 310 through 324 removed outlier: 3.908A pdb=" N GLU B 315 " --> pdb=" O THR B 311 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LEU B 316 " --> pdb=" O PRO B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 349 Processing helix chain 'B' and resid 379 through 410 removed outlier: 3.613A pdb=" N GLY B 388 " --> pdb=" O ILE B 384 " (cutoff:3.500A) Proline residue: B 405 - end of helix Processing helix chain 'B' and resid 411 through 418 removed outlier: 3.631A pdb=" N GLN B 418 " --> pdb=" O ARG B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 445 Processing helix chain 'B' and resid 450 through 464 removed outlier: 3.992A pdb=" N PHE B 456 " --> pdb=" O VAL B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 470 removed outlier: 3.787A pdb=" N ARG B 470 " --> pdb=" O TYR B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 513 removed outlier: 3.641A pdb=" N LEU B 490 " --> pdb=" O ILE B 486 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N MET B 491 " --> pdb=" O PHE B 487 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ARG B 492 " --> pdb=" O GLY B 488 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N PHE B 493 " --> pdb=" O ASP B 489 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N VAL B 499 " --> pdb=" O TRP B 495 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N VAL B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLY B 503 " --> pdb=" O VAL B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 538 removed outlier: 3.520A pdb=" N LEU B 538 " --> pdb=" O PHE B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 566 removed outlier: 3.767A pdb=" N CYS B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE B 557 " --> pdb=" O PHE B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 605 removed outlier: 3.914A pdb=" N ASN B 572 " --> pdb=" O LEU B 568 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N GLN B 587 " --> pdb=" O TRP B 583 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N GLU B 588 " --> pdb=" O ARG B 584 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLU B 591 " --> pdb=" O GLN B 587 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL B 598 " --> pdb=" O ARG B 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 47 removed outlier: 3.715A pdb=" N SER C 47 " --> pdb=" O ARG C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 56 removed outlier: 3.590A pdb=" N GLN C 51 " --> pdb=" O SER C 47 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 67 removed outlier: 3.680A pdb=" N ASN C 67 " --> pdb=" O ILE C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.732A pdb=" N TYR C 89 " --> pdb=" O VAL C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 102 removed outlier: 3.610A pdb=" N ALA C 95 " --> pdb=" O ASN C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 107 removed outlier: 3.990A pdb=" N ALA C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.732A pdb=" N ILE C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 140 Processing helix chain 'C' and resid 165 through 174 Processing helix chain 'C' and resid 175 through 184 Processing helix chain 'C' and resid 198 through 205 Processing helix chain 'C' and resid 213 through 222 Processing helix chain 'C' and resid 242 through 250 Processing helix chain 'C' and resid 252 through 264 removed outlier: 4.082A pdb=" N LYS C 262 " --> pdb=" O HIS C 258 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG C 263 " --> pdb=" O LEU C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 298 Processing helix chain 'C' and resid 303 through 308 removed outlier: 3.895A pdb=" N ILE C 307 " --> pdb=" O GLU C 303 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU C 308 " --> pdb=" O ALA C 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 303 through 308' Processing helix chain 'C' and resid 310 through 324 removed outlier: 3.912A pdb=" N GLU C 315 " --> pdb=" O THR C 311 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LEU C 316 " --> pdb=" O PRO C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 349 Processing helix chain 'C' and resid 379 through 410 removed outlier: 3.615A pdb=" N GLY C 388 " --> pdb=" O ILE C 384 " (cutoff:3.500A) Proline residue: C 405 - end of helix Processing helix chain 'C' and resid 411 through 418 removed outlier: 3.630A pdb=" N GLN C 418 " --> pdb=" O ARG C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 445 Processing helix chain 'C' and resid 450 through 464 removed outlier: 4.343A pdb=" N PHE C 456 " --> pdb=" O VAL C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 470 removed outlier: 3.847A pdb=" N ARG C 470 " --> pdb=" O TYR C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 513 removed outlier: 3.697A pdb=" N LEU C 490 " --> pdb=" O ILE C 486 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N MET C 491 " --> pdb=" O PHE C 487 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ARG C 492 " --> pdb=" O GLY C 488 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE C 493 " --> pdb=" O ASP C 489 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N VAL C 499 " --> pdb=" O TRP C 495 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N VAL C 500 " --> pdb=" O LEU C 496 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLY C 503 " --> pdb=" O VAL C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 538 removed outlier: 3.504A pdb=" N LEU C 538 " --> pdb=" O PHE C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 566 removed outlier: 3.688A pdb=" N CYS C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE C 557 " --> pdb=" O PHE C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 605 removed outlier: 3.917A pdb=" N ASN C 572 " --> pdb=" O LEU C 568 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLN C 587 " --> pdb=" O TRP C 583 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N GLU C 588 " --> pdb=" O ARG C 584 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLU C 591 " --> pdb=" O GLN C 587 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL C 598 " --> pdb=" O ARG C 594 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 47 removed outlier: 3.715A pdb=" N SER D 47 " --> pdb=" O ARG D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 56 removed outlier: 3.586A pdb=" N GLN D 51 " --> pdb=" O SER D 47 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN D 56 " --> pdb=" O ALA D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 67 removed outlier: 3.680A pdb=" N ASN D 67 " --> pdb=" O ILE D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 89 removed outlier: 3.722A pdb=" N TYR D 89 " --> pdb=" O VAL D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 102 removed outlier: 3.622A pdb=" N ALA D 95 " --> pdb=" O ASN D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 107 removed outlier: 3.990A pdb=" N ALA D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.750A pdb=" N ILE D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 140 Processing helix chain 'D' and resid 165 through 174 Processing helix chain 'D' and resid 175 through 184 Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 213 through 222 Processing helix chain 'D' and resid 242 through 251 removed outlier: 3.743A pdb=" N GLY D 251 " --> pdb=" O ALA D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 264 removed outlier: 4.080A pdb=" N LYS D 262 " --> pdb=" O HIS D 258 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG D 263 " --> pdb=" O LEU D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 298 Processing helix chain 'D' and resid 303 through 308 removed outlier: 3.865A pdb=" N ILE D 307 " --> pdb=" O GLU D 303 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 303 through 308' Processing helix chain 'D' and resid 310 through 324 removed outlier: 3.907A pdb=" N GLU D 315 " --> pdb=" O THR D 311 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LEU D 316 " --> pdb=" O PRO D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 349 Processing helix chain 'D' and resid 379 through 410 removed outlier: 3.615A pdb=" N GLY D 388 " --> pdb=" O ILE D 384 " (cutoff:3.500A) Proline residue: D 405 - end of helix Processing helix chain 'D' and resid 411 through 418 removed outlier: 3.614A pdb=" N GLN D 418 " --> pdb=" O ARG D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 445 Processing helix chain 'D' and resid 450 through 464 removed outlier: 4.344A pdb=" N PHE D 456 " --> pdb=" O VAL D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 470 removed outlier: 3.780A pdb=" N ARG D 470 " --> pdb=" O TYR D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 513 removed outlier: 3.604A pdb=" N LEU D 490 " --> pdb=" O ILE D 486 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N MET D 491 " --> pdb=" O PHE D 487 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ARG D 492 " --> pdb=" O GLY D 488 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE D 493 " --> pdb=" O ASP D 489 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL D 499 " --> pdb=" O TRP D 495 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL D 500 " --> pdb=" O LEU D 496 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLY D 503 " --> pdb=" O VAL D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 538 removed outlier: 3.518A pdb=" N LEU D 538 " --> pdb=" O PHE D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 566 removed outlier: 3.742A pdb=" N CYS D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE D 557 " --> pdb=" O PHE D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 605 removed outlier: 3.861A pdb=" N ASN D 572 " --> pdb=" O LEU D 568 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N GLN D 587 " --> pdb=" O TRP D 583 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N GLU D 588 " --> pdb=" O ARG D 584 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLU D 591 " --> pdb=" O GLN D 587 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL D 598 " --> pdb=" O ARG D 594 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 273 through 279 Processing sheet with id=AA2, first strand: chain 'A' and resid 352 through 354 Processing sheet with id=AA3, first strand: chain 'B' and resid 273 through 279 Processing sheet with id=AA4, first strand: chain 'B' and resid 352 through 354 Processing sheet with id=AA5, first strand: chain 'C' and resid 273 through 279 Processing sheet with id=AA6, first strand: chain 'C' and resid 352 through 354 Processing sheet with id=AA7, first strand: chain 'D' and resid 273 through 279 Processing sheet with id=AA8, first strand: chain 'D' and resid 352 through 354 1025 hydrogen bonds defined for protein. 3033 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: 6.09 Time building geometry restraints manager: 6.26 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: 5942 1.34 - 1.46: 3808 1.46 - 1.58: 9882 1.58 - 1.70: 0 1.70 - 1.82: 228 Bond restraints: 19860 Sorted by residual: bond pdb=" CB PHE D 574 " pdb=" CG PHE D 574 " ideal model delta sigma weight residual 1.502 1.409 0.093 2.30e-02 1.89e+03 1.65e+01 bond pdb=" CB PHE B 574 " pdb=" CG PHE B 574 " ideal model delta sigma weight residual 1.502 1.410 0.092 2.30e-02 1.89e+03 1.58e+01 bond pdb=" CB PHE C 574 " pdb=" CG PHE C 574 " ideal model delta sigma weight residual 1.502 1.416 0.086 2.30e-02 1.89e+03 1.41e+01 bond pdb=" CB PHE A 574 " pdb=" CG PHE A 574 " ideal model delta sigma weight residual 1.502 1.417 0.085 2.30e-02 1.89e+03 1.37e+01 bond pdb=" CD2 PHE A 574 " pdb=" CE2 PHE A 574 " ideal model delta sigma weight residual 1.382 1.287 0.095 3.00e-02 1.11e+03 1.00e+01 ... (remaining 19855 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.51: 26416 3.51 - 7.02: 441 7.02 - 10.53: 100 10.53 - 14.04: 3 14.04 - 17.54: 4 Bond angle restraints: 26964 Sorted by residual: angle pdb=" N ILE D 367 " pdb=" CA ILE D 367 " pdb=" C ILE D 367 " ideal model delta sigma weight residual 113.53 108.25 5.28 9.80e-01 1.04e+00 2.90e+01 angle pdb=" CA LEU C 98 " pdb=" CB LEU C 98 " pdb=" CG LEU C 98 " ideal model delta sigma weight residual 116.30 133.84 -17.54 3.50e+00 8.16e-02 2.51e+01 angle pdb=" C ASP A 223 " pdb=" N GLU A 224 " pdb=" CA GLU A 224 " ideal model delta sigma weight residual 121.54 131.08 -9.54 1.91e+00 2.74e-01 2.49e+01 angle pdb=" CA LEU A 98 " pdb=" CB LEU A 98 " pdb=" CG LEU A 98 " ideal model delta sigma weight residual 116.30 133.78 -17.48 3.50e+00 8.16e-02 2.49e+01 angle pdb=" C ASP D 223 " pdb=" N GLU D 224 " pdb=" CA GLU D 224 " ideal model delta sigma weight residual 121.54 131.05 -9.51 1.91e+00 2.74e-01 2.48e+01 ... (remaining 26959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.60: 10323 16.60 - 33.21: 1198 33.21 - 49.81: 212 49.81 - 66.41: 48 66.41 - 83.02: 31 Dihedral angle restraints: 11812 sinusoidal: 4732 harmonic: 7080 Sorted by residual: dihedral pdb=" CA PHE D 493 " pdb=" C PHE D 493 " pdb=" N CYS D 494 " pdb=" CA CYS D 494 " ideal model delta harmonic sigma weight residual 180.00 148.24 31.76 0 5.00e+00 4.00e-02 4.03e+01 dihedral pdb=" CA PHE C 493 " pdb=" C PHE C 493 " pdb=" N CYS C 494 " pdb=" CA CYS C 494 " ideal model delta harmonic sigma weight residual 180.00 148.63 31.37 0 5.00e+00 4.00e-02 3.94e+01 dihedral pdb=" CA PHE B 493 " pdb=" C PHE B 493 " pdb=" N CYS B 494 " pdb=" CA CYS B 494 " ideal model delta harmonic sigma weight residual 180.00 149.54 30.46 0 5.00e+00 4.00e-02 3.71e+01 ... (remaining 11809 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 2773 0.106 - 0.211: 261 0.211 - 0.317: 34 0.317 - 0.422: 0 0.422 - 0.528: 4 Chirality restraints: 3072 Sorted by residual: chirality pdb=" CB ILE A 575 " pdb=" CA ILE A 575 " pdb=" CG1 ILE A 575 " pdb=" CG2 ILE A 575 " both_signs ideal model delta sigma weight residual False 2.64 2.12 0.53 2.00e-01 2.50e+01 6.96e+00 chirality pdb=" CB ILE D 575 " pdb=" CA ILE D 575 " pdb=" CG1 ILE D 575 " pdb=" CG2 ILE D 575 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.47 2.00e-01 2.50e+01 5.61e+00 chirality pdb=" CB ILE C 575 " pdb=" CA ILE C 575 " pdb=" CG1 ILE C 575 " pdb=" CG2 ILE C 575 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.47 2.00e-01 2.50e+01 5.56e+00 ... (remaining 3069 not shown) Planarity restraints: 3416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 493 " -0.054 2.00e-02 2.50e+03 5.06e-02 4.49e+01 pdb=" CG PHE C 493 " 0.116 2.00e-02 2.50e+03 pdb=" CD1 PHE C 493 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE C 493 " -0.034 2.00e-02 2.50e+03 pdb=" CE1 PHE C 493 " -0.020 2.00e-02 2.50e+03 pdb=" CE2 PHE C 493 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE C 493 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 493 " -0.057 2.00e-02 2.50e+03 5.01e-02 4.40e+01 pdb=" CG PHE A 493 " 0.114 2.00e-02 2.50e+03 pdb=" CD1 PHE A 493 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 PHE A 493 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 493 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 493 " -0.022 2.00e-02 2.50e+03 pdb=" CZ PHE A 493 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 493 " 0.053 2.00e-02 2.50e+03 4.94e-02 4.27e+01 pdb=" CG PHE D 493 " -0.112 2.00e-02 2.50e+03 pdb=" CD1 PHE D 493 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE D 493 " 0.034 2.00e-02 2.50e+03 pdb=" CE1 PHE D 493 " 0.023 2.00e-02 2.50e+03 pdb=" CE2 PHE D 493 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE D 493 " 0.006 2.00e-02 2.50e+03 ... (remaining 3413 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 3971 2.78 - 3.31: 17949 3.31 - 3.84: 32596 3.84 - 4.37: 36435 4.37 - 4.90: 62630 Nonbonded interactions: 153581 Sorted by model distance: nonbonded pdb=" OE2 GLU B 522 " pdb=" OG SER B 532 " model vdw 2.245 3.040 nonbonded pdb=" OE1 GLN C 267 " pdb=" OG SER C 275 " model vdw 2.313 3.040 nonbonded pdb=" OE1 GLN B 267 " pdb=" OG SER B 275 " model vdw 2.314 3.040 nonbonded pdb=" OE1 GLN A 267 " pdb=" OG SER A 275 " model vdw 2.314 3.040 nonbonded pdb=" OE1 GLN D 267 " pdb=" OG SER D 275 " model vdw 2.314 3.040 ... (remaining 153576 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 110.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.880 Check model and map are aligned: 0.150 Set scattering table: 0.230 Process input model: 46.910 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.110 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:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 162.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 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 0.095 19860 Z= 0.298 Angle : 1.179 17.544 26964 Z= 0.613 Chirality : 0.066 0.528 3072 Planarity : 0.009 0.092 3416 Dihedral : 15.114 83.018 7236 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -4.03 (0.12), residues: 2408 helix: -2.53 (0.10), residues: 1460 sheet: -3.06 (0.46), residues: 76 loop : -2.60 (0.16), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 613 HIS 0.006 0.001 HIS C 258 PHE 0.116 0.005 PHE C 493 TYR 0.030 0.002 TYR A 467 ARG 0.016 0.001 ARG B 154 Details of bonding type rmsd hydrogen bonds : bond 0.13968 ( 1025) hydrogen bonds : angle 7.05671 ( 3033) covalent geometry : bond 0.00655 (19860) covalent geometry : angle 1.17916 (26964) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 342 time to evaluate : 2.178 Fit side-chains revert: symmetry clash REVERT: A 315 GLU cc_start: 0.8302 (tp30) cc_final: 0.8045 (tp30) REVERT: A 447 MET cc_start: 0.6885 (ppp) cc_final: 0.6550 (ppp) REVERT: A 472 PHE cc_start: 0.7893 (m-80) cc_final: 0.7682 (m-10) REVERT: A 570 MET cc_start: 0.8428 (mmm) cc_final: 0.8207 (mmm) REVERT: B 447 MET cc_start: 0.6883 (ppp) cc_final: 0.6515 (ppp) REVERT: B 481 MET cc_start: 0.7975 (mmm) cc_final: 0.7713 (tpt) REVERT: B 553 PHE cc_start: 0.8179 (t80) cc_final: 0.7673 (p90) REVERT: B 570 MET cc_start: 0.8425 (mmm) cc_final: 0.8014 (mmm) REVERT: C 447 MET cc_start: 0.6894 (ppp) cc_final: 0.6532 (ppp) REVERT: C 570 MET cc_start: 0.8326 (mmm) cc_final: 0.7992 (mmm) REVERT: D 447 MET cc_start: 0.6900 (ppp) cc_final: 0.6529 (ppp) REVERT: D 481 MET cc_start: 0.7907 (mmm) cc_final: 0.7564 (tpt) REVERT: D 570 MET cc_start: 0.8315 (mmm) cc_final: 0.8035 (mmm) outliers start: 0 outliers final: 0 residues processed: 342 average time/residue: 0.2628 time to fit residues: 146.4363 Evaluate side-chains 254 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 2.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 0.7980 chunk 181 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 122 optimal weight: 0.2980 chunk 97 optimal weight: 2.9990 chunk 188 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 114 optimal weight: 0.6980 chunk 140 optimal weight: 4.9990 chunk 217 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN A 208 ASN A 306 GLN A 582 HIS ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 ASN ** B 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 ASN C 208 ASN C 306 GLN ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN D 208 ASN ** D 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.118145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.096564 restraints weight = 42504.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.099568 restraints weight = 22555.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.101585 restraints weight = 15187.624| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19860 Z= 0.129 Angle : 0.604 7.017 26964 Z= 0.309 Chirality : 0.039 0.177 3072 Planarity : 0.005 0.041 3416 Dihedral : 4.848 27.773 2644 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.48 % Allowed : 9.69 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.15), residues: 2408 helix: -0.51 (0.13), residues: 1460 sheet: -2.41 (0.47), residues: 84 loop : -2.24 (0.18), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 495 HIS 0.009 0.001 HIS A 582 PHE 0.039 0.001 PHE A 493 TYR 0.011 0.001 TYR C 467 ARG 0.003 0.000 ARG D 302 Details of bonding type rmsd hydrogen bonds : bond 0.03893 ( 1025) hydrogen bonds : angle 4.52606 ( 3033) covalent geometry : bond 0.00287 (19860) covalent geometry : angle 0.60352 (26964) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 301 time to evaluate : 2.923 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 447 MET cc_start: 0.6850 (ppp) cc_final: 0.6334 (ppp) REVERT: A 472 PHE cc_start: 0.7927 (m-80) cc_final: 0.7717 (m-10) REVERT: A 582 HIS cc_start: 0.7054 (OUTLIER) cc_final: 0.6606 (t70) REVERT: B 447 MET cc_start: 0.6864 (ppp) cc_final: 0.6340 (ppp) REVERT: B 554 MET cc_start: 0.6900 (tpp) cc_final: 0.6674 (tpp) REVERT: C 447 MET cc_start: 0.6870 (ppp) cc_final: 0.6396 (ppp) REVERT: C 554 MET cc_start: 0.7795 (tpp) cc_final: 0.7551 (tpp) REVERT: D 340 MET cc_start: 0.9375 (mmt) cc_final: 0.9044 (mmt) REVERT: D 447 MET cc_start: 0.6866 (ppp) cc_final: 0.6360 (ppp) REVERT: D 554 MET cc_start: 0.6892 (tpp) cc_final: 0.6669 (tpp) outliers start: 31 outliers final: 23 residues processed: 318 average time/residue: 0.3331 time to fit residues: 176.3633 Evaluate side-chains 288 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 264 time to evaluate : 2.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 582 HIS Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 577 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 25 optimal weight: 7.9990 chunk 63 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 192 optimal weight: 5.9990 chunk 113 optimal weight: 0.7980 chunk 71 optimal weight: 9.9990 chunk 211 optimal weight: 0.9980 chunk 205 optimal weight: 4.9990 chunk 152 optimal weight: 5.9990 chunk 221 optimal weight: 6.9990 chunk 101 optimal weight: 8.9990 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.106057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.084545 restraints weight = 43447.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.087247 restraints weight = 23683.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.089043 restraints weight = 16269.293| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.066 19860 Z= 0.329 Angle : 0.792 7.257 26964 Z= 0.403 Chirality : 0.046 0.194 3072 Planarity : 0.005 0.032 3416 Dihedral : 4.877 16.623 2644 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.53 % Allowed : 14.74 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.17), residues: 2408 helix: 0.01 (0.13), residues: 1460 sheet: -2.83 (0.45), residues: 88 loop : -1.62 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 629 HIS 0.022 0.002 HIS A 582 PHE 0.042 0.002 PHE C 574 TYR 0.020 0.002 TYR C 467 ARG 0.005 0.001 ARG A 615 Details of bonding type rmsd hydrogen bonds : bond 0.04505 ( 1025) hydrogen bonds : angle 4.62227 ( 3033) covalent geometry : bond 0.00759 (19860) covalent geometry : angle 0.79170 (26964) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 234 time to evaluate : 4.637 Fit side-chains revert: symmetry clash REVERT: A 250 GLU cc_start: 0.8311 (tp30) cc_final: 0.7883 (tp30) REVERT: A 410 VAL cc_start: 0.8449 (t) cc_final: 0.8175 (p) REVERT: A 447 MET cc_start: 0.6879 (ppp) cc_final: 0.6484 (ppp) REVERT: A 472 PHE cc_start: 0.8568 (m-80) cc_final: 0.8289 (m-10) REVERT: B 250 GLU cc_start: 0.8342 (tp30) cc_final: 0.7972 (tp30) REVERT: B 447 MET cc_start: 0.6894 (ppp) cc_final: 0.6503 (ppp) REVERT: B 577 MET cc_start: 0.8134 (ttp) cc_final: 0.7858 (ttp) REVERT: C 250 GLU cc_start: 0.8330 (tp30) cc_final: 0.7920 (tp30) REVERT: C 447 MET cc_start: 0.6910 (ppp) cc_final: 0.6522 (ppp) REVERT: D 250 GLU cc_start: 0.8369 (tp30) cc_final: 0.8011 (tp30) REVERT: D 407 ILE cc_start: 0.8729 (tp) cc_final: 0.8510 (tt) REVERT: D 447 MET cc_start: 0.6927 (ppp) cc_final: 0.6550 (ppp) REVERT: D 472 PHE cc_start: 0.8504 (m-80) cc_final: 0.8220 (m-10) outliers start: 53 outliers final: 34 residues processed: 276 average time/residue: 0.2750 time to fit residues: 127.0261 Evaluate side-chains 240 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 206 time to evaluate : 2.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 577 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 69 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 169 optimal weight: 0.7980 chunk 218 optimal weight: 7.9990 chunk 133 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 176 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 208 ASN B 37 ASN B 91 ASN B 208 ASN ** B 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 ASN C 91 ASN ** C 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN D 208 ASN ** D 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.111617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.090264 restraints weight = 42795.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.093089 restraints weight = 23083.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.094945 restraints weight = 15757.409| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19860 Z= 0.126 Angle : 0.583 7.460 26964 Z= 0.293 Chirality : 0.040 0.155 3072 Planarity : 0.004 0.033 3416 Dihedral : 4.503 15.632 2644 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.43 % Allowed : 15.12 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.17), residues: 2408 helix: 0.60 (0.14), residues: 1452 sheet: -2.38 (0.48), residues: 84 loop : -1.55 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 593 HIS 0.004 0.001 HIS B 582 PHE 0.017 0.001 PHE D 493 TYR 0.011 0.001 TYR A 467 ARG 0.005 0.000 ARG B 584 Details of bonding type rmsd hydrogen bonds : bond 0.03434 ( 1025) hydrogen bonds : angle 4.04430 ( 3033) covalent geometry : bond 0.00283 (19860) covalent geometry : angle 0.58303 (26964) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 268 time to evaluate : 2.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 GLU cc_start: 0.8237 (tp30) cc_final: 0.7987 (tp30) REVERT: A 447 MET cc_start: 0.6819 (ppp) cc_final: 0.6361 (ppp) REVERT: A 472 PHE cc_start: 0.8416 (m-80) cc_final: 0.8130 (m-10) REVERT: A 554 MET cc_start: 0.7314 (tpp) cc_final: 0.6923 (tpp) REVERT: B 250 GLU cc_start: 0.8232 (tp30) cc_final: 0.8016 (tp30) REVERT: B 447 MET cc_start: 0.6775 (ppp) cc_final: 0.6344 (ppp) REVERT: B 554 MET cc_start: 0.6956 (tpp) cc_final: 0.6754 (tpp) REVERT: C 250 GLU cc_start: 0.8255 (tp30) cc_final: 0.8025 (tp30) REVERT: C 407 ILE cc_start: 0.8693 (tp) cc_final: 0.8481 (tt) REVERT: C 410 VAL cc_start: 0.8352 (t) cc_final: 0.8117 (p) REVERT: C 447 MET cc_start: 0.6777 (ppp) cc_final: 0.6341 (ppp) REVERT: C 554 MET cc_start: 0.7520 (tpp) cc_final: 0.7252 (tpp) REVERT: D 407 ILE cc_start: 0.8768 (tp) cc_final: 0.8512 (tt) REVERT: D 447 MET cc_start: 0.6751 (ppp) cc_final: 0.6331 (ppp) REVERT: D 472 PHE cc_start: 0.8362 (m-80) cc_final: 0.8149 (m-10) outliers start: 51 outliers final: 27 residues processed: 311 average time/residue: 0.2768 time to fit residues: 140.4405 Evaluate side-chains 266 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 239 time to evaluate : 2.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 384 ILE Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 255 MET Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 384 ILE Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 577 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 46 optimal weight: 0.8980 chunk 57 optimal weight: 0.0070 chunk 233 optimal weight: 0.6980 chunk 207 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 chunk 101 optimal weight: 2.9990 chunk 169 optimal weight: 0.5980 chunk 87 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN A 208 ASN B 91 ASN ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 ASN ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN D 208 ASN ** D 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.113131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.091679 restraints weight = 42688.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.094602 restraints weight = 22540.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.096562 restraints weight = 15162.987| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19860 Z= 0.115 Angle : 0.574 9.068 26964 Z= 0.285 Chirality : 0.039 0.194 3072 Planarity : 0.004 0.032 3416 Dihedral : 4.266 15.186 2644 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.48 % Allowed : 17.80 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.17), residues: 2408 helix: 0.93 (0.14), residues: 1444 sheet: -2.14 (0.50), residues: 84 loop : -1.49 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 495 HIS 0.008 0.001 HIS C 185 PHE 0.029 0.001 PHE C 574 TYR 0.013 0.001 TYR A 467 ARG 0.003 0.000 ARG B 584 Details of bonding type rmsd hydrogen bonds : bond 0.03216 ( 1025) hydrogen bonds : angle 3.96243 ( 3033) covalent geometry : bond 0.00258 (19860) covalent geometry : angle 0.57403 (26964) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 268 time to evaluate : 2.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASN cc_start: 0.8635 (OUTLIER) cc_final: 0.7854 (t0) REVERT: A 447 MET cc_start: 0.6820 (ppp) cc_final: 0.6364 (ppp) REVERT: A 472 PHE cc_start: 0.8349 (m-80) cc_final: 0.8028 (m-10) REVERT: A 554 MET cc_start: 0.7276 (tpp) cc_final: 0.6909 (tpp) REVERT: B 205 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7491 (mp) REVERT: B 447 MET cc_start: 0.6821 (ppp) cc_final: 0.6377 (ppp) REVERT: B 481 MET cc_start: 0.8420 (mmm) cc_final: 0.8178 (tpt) REVERT: B 554 MET cc_start: 0.6916 (tpp) cc_final: 0.6695 (tpp) REVERT: C 402 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8686 (tt) REVERT: C 407 ILE cc_start: 0.8700 (tp) cc_final: 0.8448 (tt) REVERT: C 447 MET cc_start: 0.6792 (ppp) cc_final: 0.6371 (ppp) REVERT: C 554 MET cc_start: 0.7383 (tpp) cc_final: 0.7175 (tpp) REVERT: D 407 ILE cc_start: 0.8736 (tp) cc_final: 0.8472 (tt) REVERT: D 447 MET cc_start: 0.6793 (ppp) cc_final: 0.6399 (ppp) REVERT: D 472 PHE cc_start: 0.8284 (m-80) cc_final: 0.8045 (m-10) outliers start: 52 outliers final: 30 residues processed: 310 average time/residue: 0.2635 time to fit residues: 134.0223 Evaluate side-chains 271 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 238 time to evaluate : 2.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASN Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 608 MET Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 608 MET Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 208 ASN Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 577 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 9 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 chunk 187 optimal weight: 0.0050 chunk 47 optimal weight: 1.9990 chunk 195 optimal weight: 0.9980 chunk 227 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 11 optimal weight: 8.9990 chunk 164 optimal weight: 0.8980 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN A 91 ASN A 118 GLN A 208 ASN B 91 ASN B 208 ASN ** B 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 ASN C 118 GLN C 306 GLN ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN D 118 GLN D 208 ASN ** D 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.112933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.091560 restraints weight = 42660.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.094453 restraints weight = 22491.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.096403 restraints weight = 15172.321| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19860 Z= 0.117 Angle : 0.586 9.132 26964 Z= 0.287 Chirality : 0.039 0.193 3072 Planarity : 0.004 0.032 3416 Dihedral : 4.200 15.767 2644 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.48 % Allowed : 18.65 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.17), residues: 2408 helix: 1.05 (0.14), residues: 1444 sheet: -1.97 (0.53), residues: 84 loop : -1.38 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 495 HIS 0.010 0.001 HIS A 582 PHE 0.019 0.001 PHE D 493 TYR 0.020 0.001 TYR A 415 ARG 0.002 0.000 ARG A 584 Details of bonding type rmsd hydrogen bonds : bond 0.03127 ( 1025) hydrogen bonds : angle 3.87616 ( 3033) covalent geometry : bond 0.00270 (19860) covalent geometry : angle 0.58573 (26964) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 261 time to evaluate : 2.105 Fit side-chains revert: symmetry clash REVERT: A 37 ASN cc_start: 0.8638 (OUTLIER) cc_final: 0.8032 (t0) REVERT: A 430 ILE cc_start: 0.8484 (OUTLIER) cc_final: 0.7878 (mm) REVERT: A 447 MET cc_start: 0.6825 (ppp) cc_final: 0.6363 (ppp) REVERT: A 472 PHE cc_start: 0.8347 (m-80) cc_final: 0.8031 (m-10) REVERT: A 554 MET cc_start: 0.7173 (tpp) cc_final: 0.6803 (tpp) REVERT: A 584 ARG cc_start: 0.7585 (mtm180) cc_final: 0.7317 (mtm110) REVERT: B 430 ILE cc_start: 0.8472 (OUTLIER) cc_final: 0.7901 (mm) REVERT: B 447 MET cc_start: 0.6861 (ppp) cc_final: 0.6389 (ppp) REVERT: B 554 MET cc_start: 0.6919 (tpp) cc_final: 0.6707 (tpp) REVERT: C 407 ILE cc_start: 0.8682 (tp) cc_final: 0.8437 (tt) REVERT: C 430 ILE cc_start: 0.8488 (OUTLIER) cc_final: 0.7972 (mm) REVERT: C 447 MET cc_start: 0.6810 (ppp) cc_final: 0.6371 (ppp) REVERT: C 554 MET cc_start: 0.7338 (tpp) cc_final: 0.7129 (tpp) REVERT: D 407 ILE cc_start: 0.8707 (tp) cc_final: 0.8454 (tt) REVERT: D 430 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.7891 (mm) REVERT: D 447 MET cc_start: 0.6806 (ppp) cc_final: 0.6373 (ppp) REVERT: D 472 PHE cc_start: 0.8266 (m-80) cc_final: 0.8036 (m-10) outliers start: 52 outliers final: 38 residues processed: 301 average time/residue: 0.2573 time to fit residues: 126.8177 Evaluate side-chains 287 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 244 time to evaluate : 2.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASN Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 577 MET Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 208 ASN Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 608 MET Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 608 MET Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 208 ASN Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 255 MET Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 577 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 171 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 232 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 93 optimal weight: 9.9990 chunk 102 optimal weight: 0.6980 chunk 161 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 306 GLN C 582 HIS ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 208 ASN ** D 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.112034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.090256 restraints weight = 42907.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.093165 restraints weight = 23547.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.095102 restraints weight = 16152.983| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19860 Z= 0.126 Angle : 0.593 9.377 26964 Z= 0.291 Chirality : 0.039 0.194 3072 Planarity : 0.004 0.031 3416 Dihedral : 4.173 19.621 2644 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.48 % Allowed : 20.23 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.17), residues: 2408 helix: 1.11 (0.14), residues: 1444 sheet: -1.86 (0.55), residues: 84 loop : -1.42 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 495 HIS 0.010 0.001 HIS C 582 PHE 0.023 0.001 PHE D 553 TYR 0.014 0.001 TYR A 415 ARG 0.003 0.000 ARG B 584 Details of bonding type rmsd hydrogen bonds : bond 0.03173 ( 1025) hydrogen bonds : angle 3.87762 ( 3033) covalent geometry : bond 0.00294 (19860) covalent geometry : angle 0.59267 (26964) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 241 time to evaluate : 2.238 Fit side-chains revert: symmetry clash REVERT: A 37 ASN cc_start: 0.8649 (OUTLIER) cc_final: 0.8016 (t0) REVERT: A 447 MET cc_start: 0.6903 (ppp) cc_final: 0.6419 (ppp) REVERT: A 472 PHE cc_start: 0.8356 (m-80) cc_final: 0.8036 (m-10) REVERT: A 554 MET cc_start: 0.7143 (tpp) cc_final: 0.6787 (tpp) REVERT: A 584 ARG cc_start: 0.7654 (mtm180) cc_final: 0.7402 (mtm110) REVERT: B 447 MET cc_start: 0.6947 (ppp) cc_final: 0.6471 (ppp) REVERT: B 474 MET cc_start: 0.7740 (ttp) cc_final: 0.7474 (ttp) REVERT: B 554 MET cc_start: 0.6895 (tpp) cc_final: 0.6689 (tpp) REVERT: B 584 ARG cc_start: 0.7427 (mtm180) cc_final: 0.7101 (mtm180) REVERT: C 402 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8578 (tt) REVERT: C 407 ILE cc_start: 0.8682 (tp) cc_final: 0.8448 (tt) REVERT: C 447 MET cc_start: 0.6897 (ppp) cc_final: 0.6446 (ppp) REVERT: D 407 ILE cc_start: 0.8616 (tp) cc_final: 0.8371 (tt) REVERT: D 447 MET cc_start: 0.6890 (ppp) cc_final: 0.6462 (ppp) REVERT: D 472 PHE cc_start: 0.8293 (m-80) cc_final: 0.8062 (m-10) outliers start: 52 outliers final: 39 residues processed: 283 average time/residue: 0.2632 time to fit residues: 123.1401 Evaluate side-chains 272 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 231 time to evaluate : 2.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASN Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 577 MET Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 608 MET Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 582 HIS Chi-restraints excluded: chain C residue 608 MET Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 208 ASN Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 255 MET Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 439 THR Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 577 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 80 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 86 optimal weight: 0.0370 chunk 109 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 15 optimal weight: 0.0770 chunk 77 optimal weight: 3.9990 chunk 229 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 215 optimal weight: 2.9990 overall best weight: 0.5616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN A 91 ASN ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 ASN ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 ASN C 306 GLN ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN D 208 ASN ** D 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.113115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.091995 restraints weight = 42908.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.094823 restraints weight = 23912.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.096675 restraints weight = 16553.062| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19860 Z= 0.111 Angle : 0.584 9.771 26964 Z= 0.284 Chirality : 0.038 0.147 3072 Planarity : 0.004 0.037 3416 Dihedral : 4.131 19.865 2644 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.34 % Allowed : 20.37 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.17), residues: 2408 helix: 1.12 (0.14), residues: 1452 sheet: -1.72 (0.55), residues: 84 loop : -1.37 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 495 HIS 0.019 0.001 HIS C 582 PHE 0.022 0.001 PHE C 574 TYR 0.012 0.001 TYR A 415 ARG 0.003 0.000 ARG C 584 Details of bonding type rmsd hydrogen bonds : bond 0.03048 ( 1025) hydrogen bonds : angle 3.83493 ( 3033) covalent geometry : bond 0.00252 (19860) covalent geometry : angle 0.58375 (26964) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 248 time to evaluate : 2.291 Fit side-chains REVERT: A 37 ASN cc_start: 0.8605 (OUTLIER) cc_final: 0.8074 (t0) REVERT: A 447 MET cc_start: 0.6895 (ppp) cc_final: 0.6445 (ppp) REVERT: A 472 PHE cc_start: 0.8283 (m-80) cc_final: 0.7922 (m-10) REVERT: A 554 MET cc_start: 0.7116 (tpp) cc_final: 0.6767 (tpp) REVERT: A 584 ARG cc_start: 0.7708 (mtm180) cc_final: 0.7471 (mtm110) REVERT: B 447 MET cc_start: 0.6912 (ppp) cc_final: 0.6456 (ppp) REVERT: B 474 MET cc_start: 0.7671 (ttp) cc_final: 0.7411 (ttp) REVERT: B 554 MET cc_start: 0.6852 (tpp) cc_final: 0.6645 (tpp) REVERT: C 402 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8538 (tt) REVERT: C 407 ILE cc_start: 0.8620 (tp) cc_final: 0.8383 (tt) REVERT: C 447 MET cc_start: 0.6897 (ppp) cc_final: 0.6445 (ppp) REVERT: C 554 MET cc_start: 0.7316 (tpp) cc_final: 0.6906 (tpp) REVERT: D 407 ILE cc_start: 0.8552 (tp) cc_final: 0.8302 (tt) REVERT: D 447 MET cc_start: 0.6882 (ppp) cc_final: 0.6459 (ppp) REVERT: D 472 PHE cc_start: 0.8213 (m-80) cc_final: 0.7970 (m-10) outliers start: 49 outliers final: 36 residues processed: 283 average time/residue: 0.2665 time to fit residues: 124.4059 Evaluate side-chains 277 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 239 time to evaluate : 2.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASN Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 608 MET Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 608 MET Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 208 ASN Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 255 MET Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 577 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 148 optimal weight: 0.7980 chunk 140 optimal weight: 1.9990 chunk 154 optimal weight: 0.0170 chunk 37 optimal weight: 0.0970 chunk 162 optimal weight: 0.6980 chunk 92 optimal weight: 7.9990 chunk 216 optimal weight: 0.7980 chunk 141 optimal weight: 0.9990 chunk 193 optimal weight: 0.9980 chunk 186 optimal weight: 3.9990 chunk 228 optimal weight: 0.0570 overall best weight: 0.3334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 91 ASN ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN B 37 ASN B 91 ASN ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 ASN C 91 ASN C 306 GLN ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN ** D 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.114696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.093479 restraints weight = 42737.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.096343 restraints weight = 23882.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.098244 restraints weight = 16502.974| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 19860 Z= 0.110 Angle : 0.603 12.053 26964 Z= 0.293 Chirality : 0.038 0.149 3072 Planarity : 0.004 0.041 3416 Dihedral : 4.069 19.358 2644 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.39 % Allowed : 20.32 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.17), residues: 2408 helix: 1.20 (0.14), residues: 1444 sheet: -1.56 (0.56), residues: 84 loop : -1.39 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 495 HIS 0.011 0.001 HIS D 582 PHE 0.024 0.001 PHE C 574 TYR 0.012 0.001 TYR A 415 ARG 0.004 0.000 ARG C 584 Details of bonding type rmsd hydrogen bonds : bond 0.03005 ( 1025) hydrogen bonds : angle 3.81597 ( 3033) covalent geometry : bond 0.00243 (19860) covalent geometry : angle 0.60348 (26964) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 258 time to evaluate : 2.272 Fit side-chains REVERT: A 447 MET cc_start: 0.6903 (ppp) cc_final: 0.6428 (ppp) REVERT: A 472 PHE cc_start: 0.8290 (m-80) cc_final: 0.7948 (m-10) REVERT: A 553 PHE cc_start: 0.8342 (t80) cc_final: 0.7691 (p90) REVERT: A 584 ARG cc_start: 0.7706 (mtm180) cc_final: 0.7465 (mtm110) REVERT: B 37 ASN cc_start: 0.8654 (OUTLIER) cc_final: 0.7915 (t0) REVERT: B 447 MET cc_start: 0.6878 (ppp) cc_final: 0.6397 (ppp) REVERT: B 485 MET cc_start: 0.7878 (mmt) cc_final: 0.7570 (mmp) REVERT: C 37 ASN cc_start: 0.8649 (OUTLIER) cc_final: 0.7915 (t0) REVERT: C 302 ARG cc_start: 0.8077 (tpt90) cc_final: 0.7798 (tpt90) REVERT: C 402 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8559 (tt) REVERT: C 407 ILE cc_start: 0.8637 (tp) cc_final: 0.8390 (tt) REVERT: C 447 MET cc_start: 0.6896 (ppp) cc_final: 0.6429 (ppp) REVERT: C 474 MET cc_start: 0.7741 (ttp) cc_final: 0.7455 (ttp) REVERT: C 554 MET cc_start: 0.7277 (tpp) cc_final: 0.6894 (tpp) REVERT: D 407 ILE cc_start: 0.8550 (tp) cc_final: 0.8283 (tt) REVERT: D 447 MET cc_start: 0.6881 (ppp) cc_final: 0.6437 (ppp) REVERT: D 472 PHE cc_start: 0.8178 (m-80) cc_final: 0.7941 (m-10) REVERT: D 574 PHE cc_start: 0.8009 (m-80) cc_final: 0.7766 (m-80) REVERT: D 584 ARG cc_start: 0.7449 (mtm180) cc_final: 0.7217 (ptt-90) outliers start: 50 outliers final: 34 residues processed: 292 average time/residue: 0.2592 time to fit residues: 124.3861 Evaluate side-chains 286 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 249 time to evaluate : 2.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain B residue 37 ASN Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 491 MET Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 608 MET Chi-restraints excluded: chain C residue 37 ASN Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 608 MET Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 255 MET Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain D residue 567 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 44 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 172 optimal weight: 0.9990 chunk 155 optimal weight: 0.9980 chunk 85 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 182 optimal weight: 4.9990 chunk 116 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 306 GLN ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN ** D 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.113538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.092310 restraints weight = 42893.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.095143 restraints weight = 24060.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.097013 restraints weight = 16663.505| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19860 Z= 0.124 Angle : 0.634 12.210 26964 Z= 0.303 Chirality : 0.039 0.149 3072 Planarity : 0.004 0.039 3416 Dihedral : 4.041 18.998 2644 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.96 % Allowed : 20.80 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.17), residues: 2408 helix: 1.14 (0.14), residues: 1456 sheet: -1.54 (0.55), residues: 84 loop : -1.37 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 495 HIS 0.010 0.001 HIS D 582 PHE 0.026 0.001 PHE C 574 TYR 0.010 0.001 TYR A 467 ARG 0.003 0.000 ARG B 33 Details of bonding type rmsd hydrogen bonds : bond 0.03110 ( 1025) hydrogen bonds : angle 3.89176 ( 3033) covalent geometry : bond 0.00289 (19860) covalent geometry : angle 0.63383 (26964) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 258 time to evaluate : 2.057 Fit side-chains REVERT: A 38 MET cc_start: 0.4936 (ttt) cc_final: 0.4704 (tmm) REVERT: A 447 MET cc_start: 0.6956 (ppp) cc_final: 0.6501 (ppp) REVERT: A 472 PHE cc_start: 0.8312 (m-80) cc_final: 0.7913 (m-10) REVERT: A 584 ARG cc_start: 0.7685 (mtm180) cc_final: 0.7441 (mtm110) REVERT: B 447 MET cc_start: 0.6968 (ppp) cc_final: 0.6510 (ppp) REVERT: C 302 ARG cc_start: 0.8079 (tpt90) cc_final: 0.7804 (tpt90) REVERT: C 402 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8558 (tt) REVERT: C 407 ILE cc_start: 0.8614 (tp) cc_final: 0.8388 (tt) REVERT: C 447 MET cc_start: 0.6956 (ppp) cc_final: 0.6502 (ppp) REVERT: C 474 MET cc_start: 0.7782 (ttp) cc_final: 0.7522 (ttp) REVERT: C 554 MET cc_start: 0.7325 (tpp) cc_final: 0.6947 (tpp) REVERT: D 407 ILE cc_start: 0.8552 (tp) cc_final: 0.8297 (tt) REVERT: D 447 MET cc_start: 0.6901 (ppp) cc_final: 0.6472 (ppp) REVERT: D 472 PHE cc_start: 0.8197 (m-80) cc_final: 0.7953 (m-10) outliers start: 41 outliers final: 35 residues processed: 284 average time/residue: 0.2491 time to fit residues: 115.5048 Evaluate side-chains 287 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 251 time to evaluate : 2.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 608 MET Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 608 MET Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 255 MET Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 491 MET Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain D residue 567 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 18 optimal weight: 0.2980 chunk 211 optimal weight: 4.9990 chunk 128 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 chunk 194 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 236 optimal weight: 4.9990 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 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 306 GLN ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.113766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.092639 restraints weight = 43120.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.095480 restraints weight = 24054.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.097347 restraints weight = 16625.174| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19860 Z= 0.121 Angle : 0.647 12.098 26964 Z= 0.306 Chirality : 0.040 0.248 3072 Planarity : 0.004 0.038 3416 Dihedral : 4.029 18.136 2644 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.05 % Allowed : 20.99 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.18), residues: 2408 helix: 1.15 (0.14), residues: 1456 sheet: -1.56 (0.55), residues: 84 loop : -1.27 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 462 HIS 0.013 0.001 HIS B 582 PHE 0.021 0.001 PHE D 553 TYR 0.023 0.001 TYR C 415 ARG 0.003 0.000 ARG C 584 Details of bonding type rmsd hydrogen bonds : bond 0.03079 ( 1025) hydrogen bonds : angle 3.89366 ( 3033) covalent geometry : bond 0.00281 (19860) covalent geometry : angle 0.64727 (26964) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7066.97 seconds wall clock time: 126 minutes 47.43 seconds (7607.43 seconds total)