Starting phenix.real_space_refine on Wed Apr 30 21:52:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e1t_47420/04_2025/9e1t_47420.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e1t_47420/04_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_47420/04_2025/9e1t_47420.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e1t_47420/04_2025/9e1t_47420.map" model { file = "/net/cci-nas-00/data/ceres_data/9e1t_47420/04_2025/9e1t_47420.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e1t_47420/04_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-5669/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: 9.16, per 1000 atoms: 0.91 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: 2.30 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: 1.13 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: 3.01 Time building geometry restraints manager: 2.72 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: 0.04 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: 1.050 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 27.330 Find NCS groups from input model: 0.150 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:14.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.250 ------------------------------------------------------------------------------- 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 : 1.138 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: 1.1688 time to fit residues: 320.1313 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 : 1.037 ------------------------------------------------------------------------------- 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 = 36)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.122062 restraints weight = 13592.957| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.58 r_work: 0.3464 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 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 : 1.204 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: 0.7332 (m-30) cc_final: 0.7065 (p0) REVERT: A 291 LEU cc_start: 0.7097 (tt) cc_final: 0.6359 (mm) REVERT: A 402 LEU cc_start: 0.7271 (OUTLIER) cc_final: 0.6928 (mp) REVERT: B 291 LEU cc_start: 0.7186 (tt) cc_final: 0.6487 (mm) REVERT: B 339 ASN cc_start: 0.7166 (m-40) cc_final: 0.6856 (m-40) REVERT: B 402 LEU cc_start: 0.7243 (OUTLIER) cc_final: 0.6850 (mp) REVERT: B 602 TYR cc_start: 0.6768 (m-80) cc_final: 0.6465 (m-10) outliers start: 32 outliers final: 6 residues processed: 187 average time/residue: 1.3971 time to fit residues: 283.6443 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 : 1.125 ------------------------------------------------------------------------------- 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: 2.9990 chunk 36 optimal weight: 0.9990 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: 1.9990 chunk 67 optimal weight: 0.2980 chunk 64 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 HIS ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4112 r_free = 0.4112 target = 0.159191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.125032 restraints weight = 13813.806| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.61 r_work: 0.3441 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 10306 Z= 0.107 Angle : 0.483 7.565 13988 Z= 0.257 Chirality : 0.040 0.141 1510 Planarity : 0.004 0.047 1758 Dihedral : 10.660 81.680 1400 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.43 % Allowed : 12.04 % Favored : 84.54 % 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: 0.40 (0.24), residues: 1192 helix: 0.56 (0.24), residues: 470 sheet: -0.42 (0.43), residues: 160 loop : 0.42 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 316 HIS 0.002 0.000 HIS B 705 PHE 0.017 0.001 PHE A 355 TYR 0.023 0.001 TYR A 723 ARG 0.008 0.001 ARG B 665 Details of bonding type rmsd hydrogen bonds : bond 0.03320 ( 386) hydrogen bonds : angle 4.68747 ( 1068) SS BOND : bond 0.00042 ( 2) SS BOND : angle 0.09206 ( 4) covalent geometry : bond 0.00239 (10304) covalent geometry : angle 0.48286 (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 175 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 138 time to evaluate : 1.051 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: 0.7240 (m-80) cc_final: 0.7026 (m-80) REVERT: A 275 ASP cc_start: 0.7375 (m-30) cc_final: 0.7044 (p0) REVERT: A 291 LEU cc_start: 0.7081 (tt) cc_final: 0.6173 (mp) REVERT: A 402 LEU cc_start: 0.7126 (OUTLIER) cc_final: 0.6783 (mp) REVERT: B 220 TYR cc_start: 0.7535 (m-80) cc_final: 0.7096 (m-80) REVERT: B 291 LEU cc_start: 0.7281 (tt) cc_final: 0.6518 (mm) REVERT: B 339 ASN cc_start: 0.7141 (m-40) cc_final: 0.6879 (m-40) REVERT: B 602 TYR cc_start: 0.6736 (m-80) cc_final: 0.6275 (m-10) outliers start: 37 outliers final: 9 residues processed: 164 average time/residue: 1.0816 time to fit residues: 192.7066 Evaluate side-chains 140 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 347 PHE 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 A residue 666 ASP 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: 0.3980 chunk 85 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 111 optimal weight: 0.0970 chunk 46 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 ASN B 345 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.152515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.120038 restraints weight = 13863.729| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.37 r_work: 0.3420 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10306 Z= 0.214 Angle : 0.564 10.622 13988 Z= 0.298 Chirality : 0.044 0.145 1510 Planarity : 0.004 0.039 1758 Dihedral : 10.830 81.052 1400 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.33 % Allowed : 13.89 % Favored : 82.78 % 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: 0.16 (0.24), residues: 1192 helix: 0.37 (0.23), residues: 464 sheet: -0.39 (0.44), residues: 140 loop : 0.19 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 316 HIS 0.004 0.001 HIS A 215 PHE 0.017 0.002 PHE B 625 TYR 0.031 0.002 TYR B 723 ARG 0.009 0.001 ARG A 665 Details of bonding type rmsd hydrogen bonds : bond 0.04050 ( 386) hydrogen bonds : angle 4.74316 ( 1068) SS BOND : bond 0.00071 ( 2) SS BOND : angle 0.50101 ( 4) covalent geometry : bond 0.00506 (10304) covalent geometry : angle 0.56412 (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 178 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 142 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 PHE cc_start: 0.7637 (t80) cc_final: 0.7241 (t80) REVERT: A 220 TYR cc_start: 0.7474 (m-80) cc_final: 0.7265 (m-80) REVERT: A 275 ASP cc_start: 0.7384 (m-30) cc_final: 0.7085 (p0) REVERT: A 291 LEU cc_start: 0.7191 (tt) cc_final: 0.6398 (mm) REVERT: A 338 PHE cc_start: 0.7049 (OUTLIER) cc_final: 0.6502 (t80) REVERT: A 402 LEU cc_start: 0.7259 (OUTLIER) cc_final: 0.6892 (mp) REVERT: B 220 TYR cc_start: 0.7605 (m-80) cc_final: 0.7301 (m-80) REVERT: B 291 LEU cc_start: 0.7374 (tt) cc_final: 0.6573 (mm) REVERT: B 338 PHE cc_start: 0.6823 (OUTLIER) cc_final: 0.6321 (t80) REVERT: B 619 MET cc_start: 0.7611 (OUTLIER) cc_final: 0.6861 (mpt) outliers start: 36 outliers final: 8 residues processed: 169 average time/residue: 1.1316 time to fit residues: 207.7461 Evaluate side-chains 132 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 677 PHE Chi-restraints excluded: chain A residue 679 TRP Chi-restraints excluded: chain B residue 338 PHE 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 719 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 82 optimal weight: 0.1980 chunk 35 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 96 optimal weight: 0.8980 chunk 84 optimal weight: 0.6980 chunk 46 optimal weight: 10.0000 chunk 39 optimal weight: 0.0570 chunk 65 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 GLN ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 GLN B 339 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.155599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.123231 restraints weight = 13808.194| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.44 r_work: 0.3459 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 10306 Z= 0.109 Angle : 0.512 9.048 13988 Z= 0.271 Chirality : 0.041 0.137 1510 Planarity : 0.004 0.034 1758 Dihedral : 10.520 79.030 1400 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.15 % Allowed : 15.74 % Favored : 81.11 % 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: 0.29 (0.24), residues: 1192 helix: 0.54 (0.24), residues: 464 sheet: -0.76 (0.42), residues: 160 loop : 0.40 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 316 HIS 0.002 0.000 HIS B 705 PHE 0.018 0.001 PHE A 744 TYR 0.026 0.001 TYR B 723 ARG 0.009 0.001 ARG A 665 Details of bonding type rmsd hydrogen bonds : bond 0.03279 ( 386) hydrogen bonds : angle 4.62065 ( 1068) SS BOND : bond 0.00002 ( 2) SS BOND : angle 0.27146 ( 4) covalent geometry : bond 0.00253 (10304) covalent geometry : angle 0.51220 (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 166 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 132 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 TYR cc_start: 0.7467 (m-80) cc_final: 0.7239 (m-80) REVERT: A 275 ASP cc_start: 0.7324 (m-30) cc_final: 0.7061 (p0) REVERT: A 291 LEU cc_start: 0.7239 (tt) cc_final: 0.6502 (mm) REVERT: A 402 LEU cc_start: 0.7193 (OUTLIER) cc_final: 0.6834 (mp) REVERT: B 220 TYR cc_start: 0.7612 (m-80) cc_final: 0.7211 (m-80) REVERT: B 291 LEU cc_start: 0.7377 (tt) cc_final: 0.6671 (mm) REVERT: B 402 LEU cc_start: 0.7173 (OUTLIER) cc_final: 0.6813 (mp) REVERT: B 407 TYR cc_start: 0.5455 (t80) cc_final: 0.5086 (t80) REVERT: B 619 MET cc_start: 0.7532 (OUTLIER) cc_final: 0.6721 (mpt) outliers start: 34 outliers final: 10 residues processed: 160 average time/residue: 1.1234 time to fit residues: 195.2482 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 : 1.222 ------------------------------------------------------------------------------- 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 483 ASP 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 373 VAL Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 619 MET Chi-restraints excluded: chain B residue 667 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 1 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 15 optimal weight: 9.9990 chunk 102 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 31 optimal weight: 0.0970 chunk 25 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 357 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 = 0.4101 r_free = 0.4101 target = 0.158329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.125765 restraints weight = 13858.738| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.51 r_work: 0.3455 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10306 Z= 0.114 Angle : 0.520 9.850 13988 Z= 0.271 Chirality : 0.041 0.136 1510 Planarity : 0.004 0.044 1758 Dihedral : 10.422 77.642 1400 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.43 % Allowed : 16.20 % Favored : 80.37 % 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: 0.32 (0.24), residues: 1192 helix: 0.54 (0.24), residues: 476 sheet: -0.72 (0.42), residues: 160 loop : 0.42 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 316 HIS 0.002 0.000 HIS A 163 PHE 0.018 0.001 PHE B 162 TYR 0.035 0.001 TYR B 723 ARG 0.010 0.001 ARG A 665 Details of bonding type rmsd hydrogen bonds : bond 0.03316 ( 386) hydrogen bonds : angle 4.59735 ( 1068) SS BOND : bond 0.00007 ( 2) SS BOND : angle 0.27932 ( 4) covalent geometry : bond 0.00262 (10304) covalent geometry : angle 0.52034 (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 162 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 125 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 TYR cc_start: 0.7475 (m-80) cc_final: 0.7232 (m-80) REVERT: A 275 ASP cc_start: 0.7378 (m-30) cc_final: 0.7071 (p0) REVERT: A 291 LEU cc_start: 0.7262 (tt) cc_final: 0.6361 (mm) REVERT: A 338 PHE cc_start: 0.7089 (OUTLIER) cc_final: 0.6500 (t80) REVERT: A 407 TYR cc_start: 0.5226 (t80) cc_final: 0.4837 (t80) REVERT: A 602 TYR cc_start: 0.7013 (m-80) cc_final: 0.6345 (m-80) REVERT: B 220 TYR cc_start: 0.7610 (m-80) cc_final: 0.7224 (m-80) REVERT: B 291 LEU cc_start: 0.7356 (tt) cc_final: 0.6682 (mm) REVERT: B 327 MET cc_start: 0.4609 (OUTLIER) cc_final: 0.3346 (ttt) REVERT: B 402 LEU cc_start: 0.7180 (OUTLIER) cc_final: 0.6807 (mp) REVERT: B 602 TYR cc_start: 0.6839 (m-10) cc_final: 0.6396 (m-10) outliers start: 37 outliers final: 9 residues processed: 156 average time/residue: 1.3098 time to fit residues: 222.5901 Evaluate side-chains 128 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 373 VAL 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 327 MET Chi-restraints excluded: chain B residue 343 LYS 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 667 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 21 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 94 optimal weight: 7.9990 chunk 111 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 27 optimal weight: 8.9990 chunk 63 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 273 GLN ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.157611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.124847 restraints weight = 14041.432| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 2.57 r_work: 0.3442 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 10306 Z= 0.131 Angle : 0.529 10.593 13988 Z= 0.276 Chirality : 0.041 0.134 1510 Planarity : 0.003 0.040 1758 Dihedral : 10.452 78.161 1400 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.69 % Allowed : 16.85 % Favored : 80.46 % 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 (0.24), residues: 1192 helix: 0.50 (0.24), residues: 476 sheet: -0.85 (0.42), residues: 160 loop : 0.38 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 316 HIS 0.002 0.001 HIS A 163 PHE 0.022 0.002 PHE B 744 TYR 0.027 0.001 TYR B 723 ARG 0.010 0.001 ARG A 665 Details of bonding type rmsd hydrogen bonds : bond 0.03497 ( 386) hydrogen bonds : angle 4.60324 ( 1068) SS BOND : bond 0.00020 ( 2) SS BOND : angle 0.30441 ( 4) covalent geometry : bond 0.00314 (10304) covalent geometry : angle 0.52908 (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 158 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 129 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 PHE cc_start: 0.7443 (t80) cc_final: 0.7162 (t80) REVERT: A 220 TYR cc_start: 0.7514 (m-80) cc_final: 0.7299 (m-80) REVERT: A 275 ASP cc_start: 0.7316 (m-30) cc_final: 0.7029 (p0) REVERT: A 291 LEU cc_start: 0.7282 (tt) cc_final: 0.6494 (mm) REVERT: A 338 PHE cc_start: 0.7088 (OUTLIER) cc_final: 0.6514 (t80) REVERT: A 402 LEU cc_start: 0.7252 (OUTLIER) cc_final: 0.6903 (mp) REVERT: A 407 TYR cc_start: 0.5411 (t80) cc_final: 0.5169 (t80) REVERT: A 738 MET cc_start: 0.7989 (ptt) cc_final: 0.7577 (ptt) REVERT: B 220 TYR cc_start: 0.7644 (m-80) cc_final: 0.7243 (m-80) REVERT: B 291 LEU cc_start: 0.7437 (tt) cc_final: 0.6737 (mm) REVERT: B 402 LEU cc_start: 0.7287 (OUTLIER) cc_final: 0.6911 (mp) REVERT: B 407 TYR cc_start: 0.5786 (t80) cc_final: 0.5449 (t80) REVERT: B 602 TYR cc_start: 0.6943 (m-10) cc_final: 0.6644 (m-10) outliers start: 29 outliers final: 12 residues processed: 151 average time/residue: 1.0804 time to fit residues: 177.3462 Evaluate side-chains 130 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 338 PHE 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 667 CYS Chi-restraints excluded: chain A residue 677 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 343 LYS 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 667 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 77 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 116 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 65 optimal weight: 0.0370 chunk 48 optimal weight: 6.9990 chunk 117 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 107 optimal weight: 0.1980 overall best weight: 1.2464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 GLN ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.155153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.122391 restraints weight = 13998.569| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.51 r_work: 0.3437 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 10306 Z= 0.142 Angle : 0.555 11.639 13988 Z= 0.290 Chirality : 0.042 0.150 1510 Planarity : 0.004 0.041 1758 Dihedral : 10.472 78.216 1400 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.06 % Allowed : 17.41 % Favored : 79.54 % 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: 0.14 (0.24), residues: 1192 helix: 0.45 (0.24), residues: 476 sheet: -0.97 (0.41), residues: 160 loop : 0.33 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 316 HIS 0.002 0.001 HIS B 553 PHE 0.025 0.001 PHE B 744 TYR 0.019 0.001 TYR B 407 ARG 0.010 0.001 ARG A 665 Details of bonding type rmsd hydrogen bonds : bond 0.03656 ( 386) hydrogen bonds : angle 4.63608 ( 1068) SS BOND : bond 0.00019 ( 2) SS BOND : angle 0.37189 ( 4) covalent geometry : bond 0.00335 (10304) covalent geometry : angle 0.55540 (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 159 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 126 time to evaluate : 1.128 Fit side-chains revert: symmetry clash REVERT: A 162 PHE cc_start: 0.7498 (t80) cc_final: 0.7142 (t80) REVERT: A 220 TYR cc_start: 0.7535 (m-80) cc_final: 0.7302 (m-80) REVERT: A 275 ASP cc_start: 0.7335 (m-30) cc_final: 0.7021 (p0) REVERT: A 291 LEU cc_start: 0.7294 (tt) cc_final: 0.6471 (mm) REVERT: A 407 TYR cc_start: 0.5599 (t80) cc_final: 0.5268 (t80) REVERT: A 602 TYR cc_start: 0.6989 (m-80) cc_final: 0.6456 (m-80) REVERT: A 738 MET cc_start: 0.8123 (ptt) cc_final: 0.7606 (ptt) REVERT: B 220 TYR cc_start: 0.7674 (m-80) cc_final: 0.7291 (m-80) REVERT: B 291 LEU cc_start: 0.7466 (tt) cc_final: 0.6679 (mm) REVERT: B 327 MET cc_start: 0.4097 (OUTLIER) cc_final: 0.2859 (ttt) REVERT: B 602 TYR cc_start: 0.6916 (m-10) cc_final: 0.6293 (m-10) outliers start: 33 outliers final: 14 residues processed: 153 average time/residue: 1.1521 time to fit residues: 192.4610 Evaluate side-chains 127 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 2.332 ------------------------------------------------------------------------------- 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 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 580 VAL Chi-restraints excluded: chain B residue 613 LEU 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: 2.9990 chunk 3 optimal weight: 0.0980 chunk 80 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 18 optimal weight: 10.0000 chunk 84 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 68 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 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 = 0.4069 r_free = 0.4069 target = 0.156280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.123945 restraints weight = 13943.255| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 2.52 r_work: 0.3516 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10306 Z= 0.113 Angle : 0.551 12.012 13988 Z= 0.286 Chirality : 0.041 0.155 1510 Planarity : 0.004 0.041 1758 Dihedral : 10.361 76.949 1400 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.22 % Allowed : 18.98 % Favored : 78.80 % 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: 0.24 (0.24), residues: 1192 helix: 0.54 (0.24), residues: 476 sheet: -0.94 (0.41), residues: 160 loop : 0.37 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 316 HIS 0.001 0.000 HIS B 553 PHE 0.024 0.001 PHE A 744 TYR 0.017 0.001 TYR B 407 ARG 0.011 0.000 ARG A 665 Details of bonding type rmsd hydrogen bonds : bond 0.03527 ( 386) hydrogen bonds : angle 4.63130 ( 1068) SS BOND : bond 0.00006 ( 2) SS BOND : angle 0.25611 ( 4) covalent geometry : bond 0.00258 (10304) covalent geometry : angle 0.55094 (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 145 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 1.303 Fit side-chains revert: symmetry clash REVERT: A 162 PHE cc_start: 0.7486 (t80) cc_final: 0.7099 (t80) REVERT: A 275 ASP cc_start: 0.7281 (m-30) cc_final: 0.6994 (p0) REVERT: A 291 LEU cc_start: 0.7487 (tt) cc_final: 0.6779 (mm) REVERT: A 407 TYR cc_start: 0.5412 (t80) cc_final: 0.5137 (t80) REVERT: A 602 TYR cc_start: 0.6887 (m-80) cc_final: 0.6370 (m-80) REVERT: A 738 MET cc_start: 0.8072 (ptt) cc_final: 0.7409 (ptt) REVERT: B 220 TYR cc_start: 0.7644 (m-80) cc_final: 0.7287 (m-80) REVERT: B 291 LEU cc_start: 0.7536 (tt) cc_final: 0.6828 (mm) REVERT: B 602 TYR cc_start: 0.6794 (m-10) cc_final: 0.6265 (m-10) outliers start: 24 outliers final: 10 residues processed: 143 average time/residue: 1.2159 time to fit residues: 191.5691 Evaluate side-chains 128 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 3.107 ------------------------------------------------------------------------------- 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 483 ASP Chi-restraints excluded: chain A residue 580 VAL 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 373 VAL Chi-restraints excluded: chain B residue 411 LEU 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 14 optimal weight: 0.0670 chunk 97 optimal weight: 0.0870 chunk 38 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 34 optimal weight: 5.9990 chunk 33 optimal weight: 0.3980 chunk 28 optimal weight: 4.9990 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.158221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.124694 restraints weight = 14190.796| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 2.46 r_work: 0.3489 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10306 Z= 0.108 Angle : 0.559 12.545 13988 Z= 0.285 Chirality : 0.041 0.137 1510 Planarity : 0.004 0.042 1758 Dihedral : 10.230 77.507 1400 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.02 % Allowed : 20.46 % Favored : 78.52 % 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: 0.27 (0.25), residues: 1192 helix: 0.51 (0.24), residues: 482 sheet: -0.83 (0.42), residues: 160 loop : 0.41 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP B 316 HIS 0.002 0.000 HIS A 553 PHE 0.014 0.001 PHE B 625 TYR 0.016 0.001 TYR B 407 ARG 0.010 0.000 ARG A 448 Details of bonding type rmsd hydrogen bonds : bond 0.03423 ( 386) hydrogen bonds : angle 4.57358 ( 1068) SS BOND : bond 0.00005 ( 2) SS BOND : angle 0.18292 ( 4) covalent geometry : bond 0.00242 (10304) covalent geometry : angle 0.55864 (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 141 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 130 time to evaluate : 1.191 Fit side-chains revert: symmetry clash REVERT: A 162 PHE cc_start: 0.7442 (t80) cc_final: 0.6993 (t80) REVERT: A 220 TYR cc_start: 0.7491 (m-80) cc_final: 0.7191 (m-80) REVERT: A 223 MET cc_start: 0.6908 (mtt) cc_final: 0.6692 (mtm) REVERT: A 275 ASP cc_start: 0.7321 (m-30) cc_final: 0.7015 (p0) REVERT: A 291 LEU cc_start: 0.7487 (tt) cc_final: 0.6756 (mm) REVERT: A 407 TYR cc_start: 0.5349 (t80) cc_final: 0.5064 (t80) REVERT: A 602 TYR cc_start: 0.6918 (m-80) cc_final: 0.6328 (m-80) REVERT: A 710 PRO cc_start: 0.6673 (Cg_exo) cc_final: 0.6451 (Cg_endo) REVERT: A 738 MET cc_start: 0.8074 (ptt) cc_final: 0.7587 (ptt) REVERT: B 220 TYR cc_start: 0.7635 (m-80) cc_final: 0.7273 (m-80) REVERT: B 291 LEU cc_start: 0.7448 (tt) cc_final: 0.6821 (mm) REVERT: B 602 TYR cc_start: 0.6781 (m-10) cc_final: 0.6242 (m-10) REVERT: B 710 PRO cc_start: 0.6725 (Cg_exo) cc_final: 0.6514 (Cg_endo) outliers start: 11 outliers final: 8 residues processed: 141 average time/residue: 1.0542 time to fit residues: 162.0311 Evaluate side-chains 130 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 122 time to evaluate : 1.142 ------------------------------------------------------------------------------- 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 483 ASP 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 373 VAL 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: 0.0170 chunk 43 optimal weight: 0.0370 chunk 103 optimal weight: 8.9990 chunk 115 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.5696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 ASN B 410 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.158007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.124656 restraints weight = 14105.935| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.58 r_work: 0.3478 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 10306 Z= 0.114 Angle : 0.580 12.629 13988 Z= 0.298 Chirality : 0.041 0.153 1510 Planarity : 0.003 0.042 1758 Dihedral : 10.263 75.954 1400 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.11 % Allowed : 20.46 % Favored : 78.43 % 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: 0.26 (0.24), residues: 1192 helix: 0.54 (0.24), residues: 482 sheet: -0.84 (0.42), residues: 160 loop : 0.37 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B 316 HIS 0.002 0.000 HIS B 553 PHE 0.028 0.001 PHE B 744 TYR 0.019 0.001 TYR B 407 ARG 0.010 0.000 ARG A 448 Details of bonding type rmsd hydrogen bonds : bond 0.03473 ( 386) hydrogen bonds : angle 4.52013 ( 1068) SS BOND : bond 0.00021 ( 2) SS BOND : angle 0.15526 ( 4) covalent geometry : bond 0.00262 (10304) covalent geometry : angle 0.57963 (13984) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9942.72 seconds wall clock time: 175 minutes 26.73 seconds (10526.73 seconds total)