Starting phenix.real_space_refine on Tue May 13 09:24:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e1t_47420/05_2025/9e1t_47420.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e1t_47420/05_2025/9e1t_47420.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e1t_47420/05_2025/9e1t_47420.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e1t_47420/05_2025/9e1t_47420.map" model { file = "/net/cci-nas-00/data/ceres_data/9e1t_47420/05_2025/9e1t_47420.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e1t_47420/05_2025/9e1t_47420.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mn 2 7.51 5 P 4 5.49 5 S 56 5.16 5 C 6484 2.51 5 N 1686 2.21 5 O 1800 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 10032 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4990 Classifications: {'peptide': 602} Link IDs: {'PTRANS': 24, 'TRANS': 577} Chain breaks: 2 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {' MN': 1, 'UDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B Time building chain proxies: 9.36, per 1000 atoms: 0.93 Number of scatterers: 10032 At special positions: 0 Unit cell: (100.067, 95.105, 101.721, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 2 24.99 S 56 16.00 P 4 15.00 O 1800 8.00 N 1686 7.00 C 6484 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 419 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 419 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.31 Conformation dependent library (CDL) restraints added in 1.0 seconds 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2320 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 8 sheets defined 49.2% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 146 through 164 removed outlier: 3.755A pdb=" N HIS A 163 " --> pdb=" O SER A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 190 removed outlier: 3.706A pdb=" N ILE A 181 " --> pdb=" O ILE A 177 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET A 190 " --> pdb=" O PHE A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 209 removed outlier: 3.539A pdb=" N VAL A 208 " --> pdb=" O LEU A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 225 removed outlier: 3.818A pdb=" N TYR A 220 " --> pdb=" O SER A 217 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N MET A 223 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LYS A 224 " --> pdb=" O GLY A 221 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU A 225 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 231 Processing helix chain 'A' and resid 250 through 257 removed outlier: 3.966A pdb=" N LEU A 254 " --> pdb=" O ASP A 250 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 261 Processing helix chain 'A' and resid 304 through 310 Processing helix chain 'A' and resid 311 through 328 removed outlier: 3.996A pdb=" N GLY A 326 " --> pdb=" O ARG A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 345 removed outlier: 3.674A pdb=" N ILE A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 357 Processing helix chain 'A' and resid 372 through 376 Processing helix chain 'A' and resid 396 through 406 removed outlier: 3.545A pdb=" N PHE A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 424 through 437 Processing helix chain 'A' and resid 443 through 452 removed outlier: 3.604A pdb=" N PHE A 451 " --> pdb=" O ARG A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 483 No H-bonds generated for 'chain 'A' and resid 481 through 483' Processing helix chain 'A' and resid 484 through 495 removed outlier: 4.099A pdb=" N LEU A 488 " --> pdb=" O ARG A 484 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLU A 489 " --> pdb=" O LEU A 485 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ALA A 490 " --> pdb=" O GLN A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 519 Processing helix chain 'A' and resid 520 through 526 removed outlier: 3.515A pdb=" N ARG A 526 " --> pdb=" O VAL A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 553 removed outlier: 3.622A pdb=" N HIS A 553 " --> pdb=" O VAL A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 584 removed outlier: 3.882A pdb=" N ILE A 581 " --> pdb=" O ARG A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 619 Processing helix chain 'A' and resid 630 through 637 removed outlier: 3.659A pdb=" N GLY A 633 " --> pdb=" O TRP A 630 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA A 635 " --> pdb=" O LYS A 632 " (cutoff:3.500A) Proline residue: A 636 - end of helix Processing helix chain 'A' and resid 638 through 645 removed outlier: 4.248A pdb=" N THR A 644 " --> pdb=" O ALA A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 691 removed outlier: 3.625A pdb=" N ALA A 683 " --> pdb=" O TRP A 679 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N HIS A 684 " --> pdb=" O ASN A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 717 Processing helix chain 'A' and resid 721 through 743 Processing helix chain 'A' and resid 744 through 750 removed outlier: 5.101A pdb=" N LYS A 748 " --> pdb=" O ALA A 745 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TYR A 749 " --> pdb=" O ALA A 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 164 removed outlier: 3.756A pdb=" N HIS B 163 " --> pdb=" O SER B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 190 removed outlier: 3.707A pdb=" N ILE B 181 " --> pdb=" O ILE B 177 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET B 190 " --> pdb=" O PHE B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 209 removed outlier: 3.539A pdb=" N VAL B 208 " --> pdb=" O LEU B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 225 removed outlier: 3.818A pdb=" N TYR B 220 " --> pdb=" O SER B 217 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET B 223 " --> pdb=" O TYR B 220 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LYS B 224 " --> pdb=" O GLY B 221 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU B 225 " --> pdb=" O LEU B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 231 Processing helix chain 'B' and resid 250 through 257 removed outlier: 3.966A pdb=" N LEU B 254 " --> pdb=" O ASP B 250 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 261 Processing helix chain 'B' and resid 304 through 310 Processing helix chain 'B' and resid 311 through 328 removed outlier: 3.996A pdb=" N GLY B 326 " --> pdb=" O ARG B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 345 removed outlier: 3.674A pdb=" N ILE B 337 " --> pdb=" O ALA B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 357 Processing helix chain 'B' and resid 372 through 376 Processing helix chain 'B' and resid 396 through 406 removed outlier: 3.545A pdb=" N PHE B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 413 Processing helix chain 'B' and resid 424 through 437 Processing helix chain 'B' and resid 443 through 452 removed outlier: 3.604A pdb=" N PHE B 451 " --> pdb=" O ARG B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 483 No H-bonds generated for 'chain 'B' and resid 481 through 483' Processing helix chain 'B' and resid 484 through 495 removed outlier: 4.101A pdb=" N LEU B 488 " --> pdb=" O ARG B 484 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLU B 489 " --> pdb=" O LEU B 485 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ALA B 490 " --> pdb=" O GLN B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 519 Processing helix chain 'B' and resid 520 through 526 removed outlier: 3.514A pdb=" N ARG B 526 " --> pdb=" O VAL B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 553 removed outlier: 3.621A pdb=" N HIS B 553 " --> pdb=" O VAL B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 584 removed outlier: 3.883A pdb=" N ILE B 581 " --> pdb=" O ARG B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 619 Processing helix chain 'B' and resid 630 through 637 removed outlier: 3.660A pdb=" N GLY B 633 " --> pdb=" O TRP B 630 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA B 635 " --> pdb=" O LYS B 632 " (cutoff:3.500A) Proline residue: B 636 - end of helix Processing helix chain 'B' and resid 638 through 645 removed outlier: 4.248A pdb=" N THR B 644 " --> pdb=" O ALA B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 691 removed outlier: 3.624A pdb=" N ALA B 683 " --> pdb=" O TRP B 679 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N HIS B 684 " --> pdb=" O ASN B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 717 Processing helix chain 'B' and resid 721 through 743 Processing helix chain 'B' and resid 744 through 750 removed outlier: 5.101A pdb=" N LYS B 748 " --> pdb=" O ALA B 745 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR B 749 " --> pdb=" O ALA B 746 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 194 through 200 removed outlier: 6.389A pdb=" N ILE A 138 " --> pdb=" O HIS A 169 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N HIS A 171 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL A 140 " --> pdb=" O HIS A 171 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE A 173 " --> pdb=" O VAL A 140 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE A 142 " --> pdb=" O ILE A 173 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N HIS A 139 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N LEU A 241 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ALA A 141 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N VAL A 270 " --> pdb=" O ASN A 296 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N GLY A 298 " --> pdb=" O GLY A 268 " (cutoff:3.500A) removed outlier: 10.972A pdb=" N GLY A 268 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU A 267 " --> pdb=" O TYR A 350 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 245 through 247 removed outlier: 5.976A pdb=" N VAL A 358 " --> pdb=" O HIS A 380 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 456 through 457 removed outlier: 6.781A pdb=" N ILE A 499 " --> pdb=" O GLY A 530 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N HIS A 532 " --> pdb=" O ILE A 499 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU A 501 " --> pdb=" O HIS A 532 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N VAL A 534 " --> pdb=" O LEU A 501 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N LEU A 503 " --> pdb=" O VAL A 534 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N SER A 500 " --> pdb=" O VAL A 474 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU A 476 " --> pdb=" O SER A 500 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N ALA A 502 " --> pdb=" O LEU A 476 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ALA A 478 " --> pdb=" O ALA A 502 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N VAL A 661 " --> pdb=" O LEU A 561 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N TYR A 660 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ARG A 664 " --> pdb=" O LYS A 590 " (cutoff:3.500A) removed outlier: 9.553A pdb=" N LYS A 590 " --> pdb=" O ARG A 664 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N PHE A 695 " --> pdb=" O VAL A 651 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 566 through 568 removed outlier: 6.925A pdb=" N PHE A 597 " --> pdb=" O HIS A 705 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 194 through 200 removed outlier: 6.390A pdb=" N ILE B 138 " --> pdb=" O HIS B 169 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N HIS B 171 " --> pdb=" O ILE B 138 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL B 140 " --> pdb=" O HIS B 171 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ILE B 173 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE B 142 " --> pdb=" O ILE B 173 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N HIS B 139 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N LEU B 241 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ALA B 141 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N VAL B 270 " --> pdb=" O ASN B 296 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N GLY B 298 " --> pdb=" O GLY B 268 " (cutoff:3.500A) removed outlier: 10.972A pdb=" N GLY B 268 " --> pdb=" O GLY B 298 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU B 267 " --> pdb=" O TYR B 350 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 245 through 247 removed outlier: 5.976A pdb=" N VAL B 358 " --> pdb=" O HIS B 380 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 456 through 457 removed outlier: 6.781A pdb=" N ILE B 499 " --> pdb=" O GLY B 530 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N HIS B 532 " --> pdb=" O ILE B 499 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU B 501 " --> pdb=" O HIS B 532 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N VAL B 534 " --> pdb=" O LEU B 501 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N LEU B 503 " --> pdb=" O VAL B 534 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N SER B 500 " --> pdb=" O VAL B 474 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU B 476 " --> pdb=" O SER B 500 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ALA B 502 " --> pdb=" O LEU B 476 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ALA B 478 " --> pdb=" O ALA B 502 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N VAL B 661 " --> pdb=" O LEU B 561 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N TYR B 660 " --> pdb=" O VAL B 594 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ARG B 664 " --> pdb=" O LYS B 590 " (cutoff:3.500A) removed outlier: 9.553A pdb=" N LYS B 590 " --> pdb=" O ARG B 664 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N PHE B 695 " --> pdb=" O VAL B 651 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 566 through 568 removed outlier: 6.925A pdb=" N PHE B 597 " --> pdb=" O HIS B 705 " (cutoff:3.500A) 386 hydrogen bonds defined for protein. 1068 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.02 Time building geometry restraints manager: 2.73 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: 3174 1.34 - 1.46: 1883 1.46 - 1.57: 5147 1.57 - 1.69: 6 1.69 - 1.81: 94 Bond restraints: 10304 Sorted by residual: bond pdb=" N GLY B 678 " pdb=" CA GLY B 678 " ideal model delta sigma weight residual 1.449 1.464 -0.014 1.45e-02 4.76e+03 9.73e-01 bond pdb=" N GLY A 678 " pdb=" CA GLY A 678 " ideal model delta sigma weight residual 1.449 1.463 -0.014 1.45e-02 4.76e+03 8.75e-01 bond pdb=" CA ASN B 357 " pdb=" C ASN B 357 " ideal model delta sigma weight residual 1.533 1.526 0.007 9.60e-03 1.09e+04 5.69e-01 bond pdb=" CA ASN A 357 " pdb=" C ASN A 357 " ideal model delta sigma weight residual 1.533 1.526 0.007 9.60e-03 1.09e+04 5.44e-01 bond pdb=" CB VAL A 153 " pdb=" CG1 VAL A 153 " ideal model delta sigma weight residual 1.521 1.505 0.016 3.30e-02 9.18e+02 2.50e-01 ... (remaining 10299 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.78: 13382 0.78 - 1.57: 505 1.57 - 2.35: 38 2.35 - 3.14: 47 3.14 - 3.92: 12 Bond angle restraints: 13984 Sorted by residual: angle pdb=" N ILE A 714 " pdb=" CA ILE A 714 " pdb=" C ILE A 714 " ideal model delta sigma weight residual 110.30 107.03 3.27 9.70e-01 1.06e+00 1.14e+01 angle pdb=" N ILE B 714 " pdb=" CA ILE B 714 " pdb=" C ILE B 714 " ideal model delta sigma weight residual 110.30 107.06 3.24 9.70e-01 1.06e+00 1.12e+01 angle pdb=" C ILE B 714 " pdb=" CA ILE B 714 " pdb=" CB ILE B 714 " ideal model delta sigma weight residual 111.81 115.48 -3.67 1.25e+00 6.40e-01 8.60e+00 angle pdb=" C ILE A 714 " pdb=" CA ILE A 714 " pdb=" CB ILE A 714 " ideal model delta sigma weight residual 111.81 115.43 -3.62 1.25e+00 6.40e-01 8.38e+00 angle pdb=" N THR A 715 " pdb=" CA THR A 715 " pdb=" C THR A 715 " ideal model delta sigma weight residual 111.11 114.39 -3.28 1.20e+00 6.94e-01 7.49e+00 ... (remaining 13979 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.28: 5816 15.28 - 30.56: 232 30.56 - 45.84: 52 45.84 - 61.12: 14 61.12 - 76.40: 22 Dihedral angle restraints: 6136 sinusoidal: 2552 harmonic: 3584 Sorted by residual: dihedral pdb=" CA TYR A 660 " pdb=" C TYR A 660 " pdb=" N VAL A 661 " pdb=" CA VAL A 661 " ideal model delta harmonic sigma weight residual -180.00 -162.32 -17.68 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA TYR B 660 " pdb=" C TYR B 660 " pdb=" N VAL B 661 " pdb=" CA VAL B 661 " ideal model delta harmonic sigma weight residual -180.00 -162.41 -17.59 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA VAL A 661 " pdb=" C VAL A 661 " pdb=" N VAL A 662 " pdb=" CA VAL A 662 " ideal model delta harmonic sigma weight residual 180.00 163.82 16.18 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 6133 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 896 0.027 - 0.053: 402 0.053 - 0.080: 125 0.080 - 0.106: 51 0.106 - 0.133: 36 Chirality restraints: 1510 Sorted by residual: chirality pdb=" CA VAL A 662 " pdb=" N VAL A 662 " pdb=" C VAL A 662 " pdb=" CB VAL A 662 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.42e-01 chirality pdb=" CA VAL B 662 " pdb=" N VAL B 662 " pdb=" C VAL B 662 " pdb=" CB VAL B 662 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 chirality pdb=" CA ILE B 211 " pdb=" N ILE B 211 " pdb=" C ILE B 211 " pdb=" CB ILE B 211 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.31e-01 ... (remaining 1507 not shown) Planarity restraints: 1758 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 352 " -0.018 5.00e-02 4.00e+02 2.78e-02 1.23e+00 pdb=" N PRO A 353 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 353 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 353 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 352 " -0.018 5.00e-02 4.00e+02 2.75e-02 1.21e+00 pdb=" N PRO B 353 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO B 353 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 353 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 338 " -0.005 2.00e-02 2.50e+03 1.02e-02 1.03e+00 pdb=" C PHE A 338 " 0.018 2.00e-02 2.50e+03 pdb=" O PHE A 338 " -0.007 2.00e-02 2.50e+03 pdb=" N ASN A 339 " -0.006 2.00e-02 2.50e+03 ... (remaining 1755 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 144 2.67 - 3.23: 9315 3.23 - 3.78: 15393 3.78 - 4.34: 22488 4.34 - 4.90: 36518 Nonbonded interactions: 83858 Sorted by model distance: nonbonded pdb=" OH TYR A 602 " pdb=" OH TYR B 602 " model vdw 2.108 3.040 nonbonded pdb="MN MN B 801 " pdb=" O1B UDP B 802 " model vdw 2.172 2.320 nonbonded pdb="MN MN A 900 " pdb=" O1B UDP A 901 " model vdw 2.173 2.320 nonbonded pdb=" O PHE B 677 " pdb=" OH TYR B 723 " model vdw 2.183 3.040 nonbonded pdb=" O PHE A 677 " pdb=" OH TYR A 723 " model vdw 2.183 3.040 ... (remaining 83853 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 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: 0.000 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 27.130 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 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 : 0.002 0.016 10306 Z= 0.092 Angle : 0.379 3.925 13988 Z= 0.215 Chirality : 0.039 0.133 1510 Planarity : 0.003 0.028 1758 Dihedral : 10.616 76.403 3810 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % 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: 0.55 (0.25), residues: 1192 helix: 0.64 (0.26), residues: 464 sheet: -0.12 (0.40), residues: 166 loop : 0.49 (0.27), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 316 HIS 0.002 0.001 HIS A 494 PHE 0.006 0.001 PHE B 355 TYR 0.009 0.001 TYR A 573 ARG 0.003 0.000 ARG A 547 Details of bonding type rmsd hydrogen bonds : bond 0.15558 ( 386) hydrogen bonds : angle 6.26236 ( 1068) SS BOND : bond 0.00036 ( 2) SS BOND : angle 0.35680 ( 4) covalent geometry : bond 0.00191 (10304) covalent geometry : angle 0.37942 (13984) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 GLU cc_start: 0.8347 (tt0) cc_final: 0.8139 (tm-30) REVERT: A 220 TYR cc_start: 0.7220 (m-80) cc_final: 0.7016 (m-80) REVERT: A 275 ASP cc_start: 0.7277 (m-30) cc_final: 0.6999 (p0) REVERT: A 291 LEU cc_start: 0.7120 (tt) cc_final: 0.6193 (mm) REVERT: B 179 GLU cc_start: 0.8444 (tt0) cc_final: 0.8235 (tm-30) REVERT: B 230 THR cc_start: 0.8366 (m) cc_final: 0.8140 (p) REVERT: B 275 ASP cc_start: 0.7227 (m-30) cc_final: 0.6989 (p0) REVERT: B 291 LEU cc_start: 0.7245 (tt) cc_final: 0.6342 (mm) outliers start: 0 outliers final: 0 residues processed: 255 average time/residue: 1.1008 time to fit residues: 302.4648 Evaluate side-chains 158 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 50 optimal weight: 0.3980 chunk 31 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 108 optimal weight: 5.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 169 HIS A 264 GLN A 359 GLN A 494 HIS A 553 HIS A 634 HIS A 705 HIS B 163 HIS B 169 HIS ** B 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 GLN B 359 GLN B 494 HIS B 553 HIS B 705 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.157966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.122063 restraints weight = 13592.956| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.58 r_work: 0.3465 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10306 Z= 0.142 Angle : 0.534 9.878 13988 Z= 0.283 Chirality : 0.042 0.142 1510 Planarity : 0.004 0.030 1758 Dihedral : 10.760 82.264 1400 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.96 % Allowed : 11.30 % Favored : 85.74 % 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: 0.45 (0.24), residues: 1192 helix: 0.58 (0.24), residues: 470 sheet: -0.33 (0.43), residues: 160 loop : 0.46 (0.27), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 316 HIS 0.004 0.001 HIS B 494 PHE 0.020 0.001 PHE A 355 TYR 0.011 0.001 TYR B 370 ARG 0.008 0.001 ARG A 665 Details of bonding type rmsd hydrogen bonds : bond 0.03778 ( 386) hydrogen bonds : angle 4.87663 ( 1068) SS BOND : bond 0.00084 ( 2) SS BOND : angle 0.04632 ( 4) covalent geometry : bond 0.00328 (10304) covalent geometry : angle 0.53443 (13984) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 163 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 ASP cc_start: 0.7327 (m-30) cc_final: 0.7065 (p0) REVERT: A 291 LEU cc_start: 0.7103 (tt) cc_final: 0.6366 (mm) REVERT: A 402 LEU cc_start: 0.7272 (OUTLIER) cc_final: 0.6930 (mp) REVERT: B 291 LEU cc_start: 0.7190 (tt) cc_final: 0.6493 (mm) REVERT: B 339 ASN cc_start: 0.7167 (m-40) cc_final: 0.6859 (m-40) REVERT: B 402 LEU cc_start: 0.7245 (OUTLIER) cc_final: 0.6852 (mp) REVERT: B 602 TYR cc_start: 0.6767 (m-80) cc_final: 0.6463 (m-10) outliers start: 32 outliers final: 6 residues processed: 187 average time/residue: 1.0519 time to fit residues: 213.4619 Evaluate side-chains 142 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 134 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 666 ASP Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 719 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 68 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 2 optimal weight: 0.4980 chunk 14 optimal weight: 7.9990 chunk 31 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 67 optimal weight: 7.9990 chunk 64 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 ASN A 454 HIS A 457 HIS B 454 HIS B 457 HIS B 634 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.158327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.124101 restraints weight = 13829.829| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 2.67 r_work: 0.3434 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10306 Z= 0.120 Angle : 0.492 7.636 13988 Z= 0.262 Chirality : 0.041 0.139 1510 Planarity : 0.004 0.045 1758 Dihedral : 10.721 81.751 1400 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.52 % Allowed : 11.85 % Favored : 84.63 % 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: 0.35 (0.24), residues: 1192 helix: 0.52 (0.24), residues: 470 sheet: -0.47 (0.43), residues: 160 loop : 0.41 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 316 HIS 0.003 0.001 HIS B 705 PHE 0.017 0.001 PHE A 355 TYR 0.024 0.001 TYR A 723 ARG 0.008 0.001 ARG B 665 Details of bonding type rmsd hydrogen bonds : bond 0.03461 ( 386) hydrogen bonds : angle 4.70130 ( 1068) SS BOND : bond 0.00053 ( 2) SS BOND : angle 0.14239 ( 4) covalent geometry : bond 0.00277 (10304) covalent geometry : angle 0.49247 (13984) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 140 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 TYR cc_start: 0.7302 (m-80) cc_final: 0.7088 (m-80) REVERT: A 275 ASP cc_start: 0.7371 (m-30) cc_final: 0.7052 (p0) REVERT: A 291 LEU cc_start: 0.7123 (tt) cc_final: 0.6234 (mm) REVERT: A 338 PHE cc_start: 0.6773 (OUTLIER) cc_final: 0.6218 (t80) REVERT: A 402 LEU cc_start: 0.7187 (OUTLIER) cc_final: 0.6836 (mp) REVERT: B 220 TYR cc_start: 0.7563 (m-80) cc_final: 0.7176 (m-80) REVERT: B 291 LEU cc_start: 0.7311 (tt) cc_final: 0.6563 (mm) REVERT: B 339 ASN cc_start: 0.7167 (m-40) cc_final: 0.6892 (m-40) REVERT: B 602 TYR cc_start: 0.6838 (m-80) cc_final: 0.6248 (m-10) outliers start: 38 outliers final: 8 residues processed: 168 average time/residue: 1.0082 time to fit residues: 184.3733 Evaluate side-chains 142 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 132 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 719 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 3 optimal weight: 3.9990 chunk 41 optimal weight: 0.0980 chunk 85 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 56 optimal weight: 0.4980 chunk 111 optimal weight: 0.9980 chunk 46 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 HIS B 345 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.156873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.122828 restraints weight = 13763.501| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 2.50 r_work: 0.3464 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 10306 Z= 0.106 Angle : 0.486 10.347 13988 Z= 0.257 Chirality : 0.040 0.139 1510 Planarity : 0.003 0.037 1758 Dihedral : 10.563 79.958 1400 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.06 % Allowed : 13.89 % Favored : 83.06 % 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: 0.31 (0.24), residues: 1192 helix: 0.45 (0.23), residues: 482 sheet: -0.43 (0.43), residues: 160 loop : 0.40 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 316 HIS 0.003 0.000 HIS B 163 PHE 0.017 0.001 PHE B 162 TYR 0.029 0.001 TYR B 723 ARG 0.009 0.001 ARG B 665 Details of bonding type rmsd hydrogen bonds : bond 0.03185 ( 386) hydrogen bonds : angle 4.60742 ( 1068) SS BOND : bond 0.00020 ( 2) SS BOND : angle 0.17519 ( 4) covalent geometry : bond 0.00245 (10304) covalent geometry : angle 0.48638 (13984) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 138 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 TYR cc_start: 0.7325 (m-80) cc_final: 0.7086 (m-80) REVERT: A 275 ASP cc_start: 0.7350 (m-30) cc_final: 0.7045 (p0) REVERT: A 291 LEU cc_start: 0.7099 (tt) cc_final: 0.6386 (mm) REVERT: A 402 LEU cc_start: 0.7185 (OUTLIER) cc_final: 0.6831 (mp) REVERT: B 220 TYR cc_start: 0.7559 (m-80) cc_final: 0.7116 (m-80) REVERT: B 291 LEU cc_start: 0.7319 (tt) cc_final: 0.6483 (mp) REVERT: B 339 ASN cc_start: 0.7156 (m-40) cc_final: 0.6857 (m-40) REVERT: B 619 MET cc_start: 0.7598 (OUTLIER) cc_final: 0.6829 (mpt) REVERT: B 710 PRO cc_start: 0.6661 (Cg_exo) cc_final: 0.6417 (Cg_endo) outliers start: 33 outliers final: 6 residues processed: 162 average time/residue: 1.0508 time to fit residues: 185.0807 Evaluate side-chains 138 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 130 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 666 ASP Chi-restraints excluded: chain A residue 677 PHE Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 619 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 82 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 chunk 39 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 16 optimal weight: 0.0670 chunk 37 optimal weight: 0.9990 overall best weight: 0.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.156387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.123765 restraints weight = 13889.460| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.50 r_work: 0.3495 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10306 Z= 0.123 Angle : 0.507 8.956 13988 Z= 0.268 Chirality : 0.041 0.135 1510 Planarity : 0.004 0.036 1758 Dihedral : 10.520 79.890 1400 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.33 % Allowed : 15.09 % Favored : 81.57 % 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: 0.20 (0.24), residues: 1192 helix: 0.34 (0.23), residues: 494 sheet: -0.52 (0.43), residues: 160 loop : 0.37 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 316 HIS 0.002 0.001 HIS B 705 PHE 0.019 0.001 PHE A 744 TYR 0.039 0.001 TYR B 723 ARG 0.009 0.001 ARG B 665 Details of bonding type rmsd hydrogen bonds : bond 0.03333 ( 386) hydrogen bonds : angle 4.56220 ( 1068) SS BOND : bond 0.00019 ( 2) SS BOND : angle 0.27702 ( 4) covalent geometry : bond 0.00285 (10304) covalent geometry : angle 0.50697 (13984) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 134 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 TYR cc_start: 0.7419 (m-80) cc_final: 0.7161 (m-80) REVERT: A 275 ASP cc_start: 0.7311 (m-30) cc_final: 0.7045 (p0) REVERT: A 291 LEU cc_start: 0.7235 (tt) cc_final: 0.6484 (mm) REVERT: A 402 LEU cc_start: 0.7284 (OUTLIER) cc_final: 0.6912 (mp) REVERT: A 602 TYR cc_start: 0.7144 (m-10) cc_final: 0.6635 (m-80) REVERT: A 738 MET cc_start: 0.8004 (ptt) cc_final: 0.7502 (ptt) REVERT: B 220 TYR cc_start: 0.7595 (m-80) cc_final: 0.7179 (m-80) REVERT: B 291 LEU cc_start: 0.7355 (tt) cc_final: 0.6709 (mm) REVERT: B 402 LEU cc_start: 0.7214 (OUTLIER) cc_final: 0.6847 (mp) REVERT: B 407 TYR cc_start: 0.5384 (t80) cc_final: 0.5062 (t80) REVERT: B 602 TYR cc_start: 0.6942 (m-80) cc_final: 0.6656 (m-10) REVERT: B 619 MET cc_start: 0.7562 (OUTLIER) cc_final: 0.6759 (mpt) REVERT: B 740 ARG cc_start: 0.8075 (mtt90) cc_final: 0.7843 (mtt90) outliers start: 36 outliers final: 10 residues processed: 164 average time/residue: 1.0000 time to fit residues: 179.3176 Evaluate side-chains 132 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 667 CYS Chi-restraints excluded: chain A residue 677 PHE Chi-restraints excluded: chain A residue 679 TRP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 619 MET Chi-restraints excluded: chain B residue 679 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 1 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 15 optimal weight: 9.9990 chunk 102 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 116 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 339 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.157288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.124256 restraints weight = 13976.831| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 2.60 r_work: 0.3452 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 10306 Z= 0.118 Angle : 0.517 10.280 13988 Z= 0.269 Chirality : 0.041 0.135 1510 Planarity : 0.003 0.037 1758 Dihedral : 10.524 79.202 1400 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.52 % Allowed : 16.30 % Favored : 80.19 % 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: 0.35 (0.24), residues: 1192 helix: 0.54 (0.24), residues: 478 sheet: -0.59 (0.43), residues: 160 loop : 0.42 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 316 HIS 0.002 0.000 HIS A 705 PHE 0.025 0.001 PHE B 162 TYR 0.038 0.001 TYR B 723 ARG 0.009 0.000 ARG B 665 Details of bonding type rmsd hydrogen bonds : bond 0.03351 ( 386) hydrogen bonds : angle 4.58005 ( 1068) SS BOND : bond 0.00007 ( 2) SS BOND : angle 0.29525 ( 4) covalent geometry : bond 0.00278 (10304) covalent geometry : angle 0.51713 (13984) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 128 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 PHE cc_start: 0.7577 (t80) cc_final: 0.7143 (t80) REVERT: A 220 TYR cc_start: 0.7445 (m-80) cc_final: 0.7210 (m-80) REVERT: A 275 ASP cc_start: 0.7325 (m-30) cc_final: 0.7026 (p0) REVERT: A 291 LEU cc_start: 0.7219 (tt) cc_final: 0.6311 (mp) REVERT: A 407 TYR cc_start: 0.5690 (t80) cc_final: 0.5264 (t80) REVERT: A 602 TYR cc_start: 0.7170 (m-10) cc_final: 0.6886 (m-80) REVERT: A 738 MET cc_start: 0.8148 (ptt) cc_final: 0.7530 (ptt) REVERT: B 220 TYR cc_start: 0.7562 (m-80) cc_final: 0.7152 (m-80) REVERT: B 291 LEU cc_start: 0.7356 (tt) cc_final: 0.6691 (mm) REVERT: B 327 MET cc_start: 0.4576 (OUTLIER) cc_final: 0.3352 (ttt) REVERT: B 402 LEU cc_start: 0.7168 (OUTLIER) cc_final: 0.6803 (mp) REVERT: B 407 TYR cc_start: 0.5521 (t80) cc_final: 0.5037 (t80) REVERT: B 619 MET cc_start: 0.7574 (OUTLIER) cc_final: 0.6785 (mpt) REVERT: B 740 ARG cc_start: 0.8132 (mtt90) cc_final: 0.7927 (mtt90) outliers start: 38 outliers final: 11 residues processed: 158 average time/residue: 0.9513 time to fit residues: 164.7905 Evaluate side-chains 126 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 677 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 327 MET Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 619 MET Chi-restraints excluded: chain B residue 667 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 21 optimal weight: 0.6980 chunk 109 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 94 optimal weight: 6.9990 chunk 111 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 118 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 335 GLN ** 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 = 0.4052 r_free = 0.4052 target = 0.154789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.121728 restraints weight = 14224.784| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.57 r_work: 0.3474 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10306 Z= 0.140 Angle : 0.538 10.840 13988 Z= 0.281 Chirality : 0.041 0.144 1510 Planarity : 0.004 0.043 1758 Dihedral : 10.498 79.205 1400 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.87 % Allowed : 17.41 % 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: 0.31 (0.24), residues: 1192 helix: 0.51 (0.24), residues: 478 sheet: -0.70 (0.42), residues: 160 loop : 0.44 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 316 HIS 0.002 0.001 HIS A 215 PHE 0.022 0.001 PHE B 744 TYR 0.024 0.001 TYR B 723 ARG 0.010 0.001 ARG A 448 Details of bonding type rmsd hydrogen bonds : bond 0.03544 ( 386) hydrogen bonds : angle 4.61297 ( 1068) SS BOND : bond 0.00022 ( 2) SS BOND : angle 0.36023 ( 4) covalent geometry : bond 0.00330 (10304) covalent geometry : angle 0.53839 (13984) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 121 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 PHE cc_start: 0.7516 (t80) cc_final: 0.7027 (t80) REVERT: A 220 TYR cc_start: 0.7488 (m-80) cc_final: 0.7243 (m-80) REVERT: A 275 ASP cc_start: 0.7324 (m-30) cc_final: 0.7043 (p0) REVERT: A 291 LEU cc_start: 0.7278 (tt) cc_final: 0.6373 (mp) REVERT: A 402 LEU cc_start: 0.7229 (OUTLIER) cc_final: 0.6888 (mp) REVERT: A 407 TYR cc_start: 0.5693 (t80) cc_final: 0.5290 (t80) REVERT: A 449 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7509 (mt-10) REVERT: A 602 TYR cc_start: 0.7195 (m-10) cc_final: 0.6899 (m-80) REVERT: A 738 MET cc_start: 0.8124 (ptt) cc_final: 0.7518 (ptt) REVERT: B 162 PHE cc_start: 0.7420 (t80) cc_final: 0.7120 (t80) REVERT: B 220 TYR cc_start: 0.7654 (m-80) cc_final: 0.7281 (m-80) REVERT: B 291 LEU cc_start: 0.7454 (tt) cc_final: 0.6721 (mm) REVERT: B 327 MET cc_start: 0.4647 (OUTLIER) cc_final: 0.3178 (ttt) REVERT: B 407 TYR cc_start: 0.5496 (t80) cc_final: 0.4991 (t80) REVERT: B 619 MET cc_start: 0.7581 (OUTLIER) cc_final: 0.6793 (mpt) REVERT: B 740 ARG cc_start: 0.8114 (mtt90) cc_final: 0.7910 (mtt90) outliers start: 31 outliers final: 15 residues processed: 148 average time/residue: 0.9633 time to fit residues: 155.7975 Evaluate side-chains 128 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 449 GLU Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 667 CYS Chi-restraints excluded: chain A residue 677 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 327 MET Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 619 MET Chi-restraints excluded: chain B residue 667 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 77 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 chunk 106 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 48 optimal weight: 6.9990 chunk 117 optimal weight: 0.8980 chunk 46 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.155049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.122006 restraints weight = 14051.815| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.57 r_work: 0.3460 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10306 Z= 0.143 Angle : 0.545 11.457 13988 Z= 0.284 Chirality : 0.042 0.152 1510 Planarity : 0.003 0.044 1758 Dihedral : 10.471 79.619 1400 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.61 % Allowed : 16.20 % Favored : 80.19 % 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: 0.22 (0.25), residues: 1192 helix: 0.44 (0.24), residues: 478 sheet: -0.86 (0.42), residues: 160 loop : 0.43 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 316 HIS 0.002 0.001 HIS B 215 PHE 0.024 0.002 PHE B 744 TYR 0.020 0.001 TYR B 723 ARG 0.010 0.001 ARG A 448 Details of bonding type rmsd hydrogen bonds : bond 0.03610 ( 386) hydrogen bonds : angle 4.62780 ( 1068) SS BOND : bond 0.00028 ( 2) SS BOND : angle 0.36571 ( 4) covalent geometry : bond 0.00337 (10304) covalent geometry : angle 0.54483 (13984) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 121 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 PHE cc_start: 0.7571 (t80) cc_final: 0.7036 (t80) REVERT: A 220 TYR cc_start: 0.7529 (m-80) cc_final: 0.7303 (m-80) REVERT: A 275 ASP cc_start: 0.7326 (m-30) cc_final: 0.7052 (p0) REVERT: A 291 LEU cc_start: 0.7324 (tt) cc_final: 0.6498 (mm) REVERT: A 407 TYR cc_start: 0.5668 (t80) cc_final: 0.5290 (t80) REVERT: A 449 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7547 (mt-10) REVERT: A 602 TYR cc_start: 0.7155 (m-10) cc_final: 0.6869 (m-80) REVERT: A 738 MET cc_start: 0.8096 (ptt) cc_final: 0.7602 (ptt) REVERT: B 162 PHE cc_start: 0.7443 (t80) cc_final: 0.7137 (t80) REVERT: B 220 TYR cc_start: 0.7687 (m-80) cc_final: 0.7292 (m-80) REVERT: B 291 LEU cc_start: 0.7438 (tt) cc_final: 0.6697 (mm) REVERT: B 407 TYR cc_start: 0.5621 (t80) cc_final: 0.5108 (t80) REVERT: B 619 MET cc_start: 0.7515 (OUTLIER) cc_final: 0.6736 (mpt) REVERT: B 740 ARG cc_start: 0.8073 (mtt90) cc_final: 0.7862 (mtt90) outliers start: 39 outliers final: 11 residues processed: 153 average time/residue: 1.0252 time to fit residues: 171.0504 Evaluate side-chains 125 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 449 GLU Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 667 CYS Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 619 MET Chi-restraints excluded: chain B residue 667 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 20 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 5 optimal weight: 0.3980 chunk 18 optimal weight: 9.9990 chunk 84 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 680 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.155096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.123005 restraints weight = 14061.036| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 2.39 r_work: 0.3496 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 10306 Z= 0.133 Angle : 0.570 12.423 13988 Z= 0.298 Chirality : 0.042 0.141 1510 Planarity : 0.003 0.041 1758 Dihedral : 10.459 78.626 1400 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.76 % Allowed : 18.61 % Favored : 79.63 % 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 (0.25), residues: 1192 helix: 0.46 (0.24), residues: 478 sheet: -0.95 (0.41), residues: 160 loop : 0.39 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 316 HIS 0.002 0.001 HIS B 553 PHE 0.026 0.002 PHE B 744 TYR 0.017 0.001 TYR B 723 ARG 0.009 0.000 ARG A 448 Details of bonding type rmsd hydrogen bonds : bond 0.03606 ( 386) hydrogen bonds : angle 4.62000 ( 1068) SS BOND : bond 0.00016 ( 2) SS BOND : angle 0.29330 ( 4) covalent geometry : bond 0.00317 (10304) covalent geometry : angle 0.56989 (13984) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 PHE cc_start: 0.7603 (t80) cc_final: 0.6992 (t80) REVERT: A 220 TYR cc_start: 0.7523 (m-80) cc_final: 0.7294 (m-80) REVERT: A 275 ASP cc_start: 0.7326 (m-30) cc_final: 0.7061 (p0) REVERT: A 291 LEU cc_start: 0.7350 (tt) cc_final: 0.6530 (mm) REVERT: A 327 MET cc_start: 0.4368 (tpt) cc_final: 0.4114 (tpp) REVERT: A 407 TYR cc_start: 0.5639 (t80) cc_final: 0.5314 (t80) REVERT: A 449 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7526 (mt-10) REVERT: A 602 TYR cc_start: 0.7129 (m-10) cc_final: 0.6864 (m-80) REVERT: A 679 TRP cc_start: 0.8225 (OUTLIER) cc_final: 0.6875 (t60) REVERT: A 738 MET cc_start: 0.8039 (ptt) cc_final: 0.7473 (ptt) REVERT: B 162 PHE cc_start: 0.7494 (t80) cc_final: 0.7082 (t80) REVERT: B 220 TYR cc_start: 0.7718 (m-80) cc_final: 0.7325 (m-80) REVERT: B 291 LEU cc_start: 0.7439 (tt) cc_final: 0.6696 (mm) REVERT: B 407 TYR cc_start: 0.5620 (t80) cc_final: 0.5155 (t80) REVERT: B 619 MET cc_start: 0.7532 (OUTLIER) cc_final: 0.6747 (mpt) REVERT: B 679 TRP cc_start: 0.8191 (OUTLIER) cc_final: 0.6968 (t60) REVERT: B 740 ARG cc_start: 0.8069 (mtt90) cc_final: 0.7819 (mtt90) outliers start: 19 outliers final: 9 residues processed: 138 average time/residue: 0.9637 time to fit residues: 145.3126 Evaluate side-chains 129 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 449 GLU Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 667 CYS Chi-restraints excluded: chain A residue 679 TRP Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 619 MET Chi-restraints excluded: chain B residue 667 CYS Chi-restraints excluded: chain B residue 679 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 14 optimal weight: 5.9990 chunk 97 optimal weight: 0.3980 chunk 38 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 72 optimal weight: 0.1980 chunk 1 optimal weight: 0.7980 chunk 34 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 ASN B 680 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.156777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.122681 restraints weight = 14221.332| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 2.61 r_work: 0.3489 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 10306 Z= 0.116 Angle : 0.574 12.811 13988 Z= 0.298 Chirality : 0.041 0.141 1510 Planarity : 0.003 0.042 1758 Dihedral : 10.327 77.933 1400 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.48 % Allowed : 19.63 % Favored : 78.89 % 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 (0.25), residues: 1192 helix: 0.49 (0.24), residues: 482 sheet: -0.89 (0.41), residues: 160 loop : 0.40 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A 316 HIS 0.002 0.000 HIS B 259 PHE 0.020 0.001 PHE A 460 TYR 0.012 0.001 TYR B 723 ARG 0.010 0.000 ARG A 448 Details of bonding type rmsd hydrogen bonds : bond 0.03473 ( 386) hydrogen bonds : angle 4.65437 ( 1068) SS BOND : bond 0.00003 ( 2) SS BOND : angle 0.21240 ( 4) covalent geometry : bond 0.00271 (10304) covalent geometry : angle 0.57428 (13984) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 PHE cc_start: 0.7628 (t80) cc_final: 0.6979 (t80) REVERT: A 220 TYR cc_start: 0.7481 (m-80) cc_final: 0.7261 (m-80) REVERT: A 275 ASP cc_start: 0.7348 (m-30) cc_final: 0.7066 (p0) REVERT: A 291 LEU cc_start: 0.7332 (tt) cc_final: 0.6481 (mm) REVERT: A 327 MET cc_start: 0.4348 (tpt) cc_final: 0.4091 (tpp) REVERT: A 407 TYR cc_start: 0.5625 (t80) cc_final: 0.5393 (t80) REVERT: A 449 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7531 (mt-10) REVERT: A 602 TYR cc_start: 0.7127 (m-10) cc_final: 0.6652 (m-80) REVERT: A 710 PRO cc_start: 0.6679 (Cg_exo) cc_final: 0.6455 (Cg_endo) REVERT: A 738 MET cc_start: 0.8020 (ptt) cc_final: 0.7419 (ptt) REVERT: B 220 TYR cc_start: 0.7715 (m-80) cc_final: 0.7320 (m-80) REVERT: B 291 LEU cc_start: 0.7390 (tt) cc_final: 0.6658 (mm) REVERT: B 602 TYR cc_start: 0.6995 (m-80) cc_final: 0.6637 (m-10) REVERT: B 619 MET cc_start: 0.7485 (OUTLIER) cc_final: 0.6696 (mpt) REVERT: B 710 PRO cc_start: 0.6737 (Cg_exo) cc_final: 0.6517 (Cg_endo) REVERT: B 740 ARG cc_start: 0.8123 (mtt90) cc_final: 0.7892 (mtt90) outliers start: 16 outliers final: 7 residues processed: 141 average time/residue: 0.9401 time to fit residues: 145.3206 Evaluate side-chains 132 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 123 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 449 GLU Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 667 CYS Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 619 MET Chi-restraints excluded: chain B residue 667 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 103 optimal weight: 7.9990 chunk 115 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 GLN ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 GLN B 335 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.153699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.120970 restraints weight = 14170.305| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.53 r_work: 0.3462 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 10306 Z= 0.175 Angle : 0.610 13.130 13988 Z= 0.317 Chirality : 0.043 0.143 1510 Planarity : 0.004 0.045 1758 Dihedral : 10.523 81.163 1400 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.76 % Allowed : 19.63 % Favored : 78.61 % 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: 0.03 (0.24), residues: 1192 helix: 0.40 (0.24), residues: 476 sheet: -1.09 (0.41), residues: 160 loop : 0.24 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 316 HIS 0.003 0.001 HIS B 532 PHE 0.026 0.002 PHE B 744 TYR 0.017 0.002 TYR B 723 ARG 0.010 0.001 ARG A 448 Details of bonding type rmsd hydrogen bonds : bond 0.03957 ( 386) hydrogen bonds : angle 4.65968 ( 1068) SS BOND : bond 0.00045 ( 2) SS BOND : angle 0.39846 ( 4) covalent geometry : bond 0.00423 (10304) covalent geometry : angle 0.60973 (13984) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8282.59 seconds wall clock time: 143 minutes 2.92 seconds (8582.92 seconds total)