Starting phenix.real_space_refine on Wed Sep 17 17:05:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e1t_47420/09_2025/9e1t_47420.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e1t_47420/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9e1t_47420/09_2025/9e1t_47420.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e1t_47420/09_2025/9e1t_47420.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9e1t_47420/09_2025/9e1t_47420.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e1t_47420/09_2025/9e1t_47420.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.59, per 1000 atoms: 0.36 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: 0.85 Conformation dependent library (CDL) restraints added in 350.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.49 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: 1.74 Time building geometry restraints manager: 1.05 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: 0.02 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: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.560 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 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:6.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.050 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG A 547 TYR 0.009 0.001 TYR A 573 PHE 0.006 0.001 PHE B 355 TRP 0.008 0.001 TRP B 316 HIS 0.002 0.001 HIS A 494 Details of bonding type rmsd covalent geometry : bond 0.00191 (10304) covalent geometry : angle 0.37942 (13984) SS BOND : bond 0.00036 ( 2) SS BOND : angle 0.35680 ( 4) hydrogen bonds : bond 0.15558 ( 386) hydrogen bonds : angle 6.26236 ( 1068) *********************** 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 : 0.395 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: 0.7015 (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: A 425 VAL cc_start: 0.8281 (t) cc_final: 0.7886 (p) 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: 0.5613 time to fit residues: 153.4428 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 : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 113 optimal weight: 0.0670 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 117 optimal weight: 0.9980 overall best weight: 1.7922 ------------------------------------------------------------------------------- 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 359 GLN B 494 HIS B 553 HIS B 705 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.155968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.120365 restraints weight = 13714.142| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.67 r_work: 0.3435 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10306 Z= 0.182 Angle : 0.558 9.822 13988 Z= 0.298 Chirality : 0.043 0.140 1510 Planarity : 0.004 0.028 1758 Dihedral : 10.895 82.118 1400 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.87 % Allowed : 11.30 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.24), residues: 1192 helix: 0.52 (0.24), residues: 468 sheet: -0.45 (0.43), residues: 160 loop : 0.38 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 665 TYR 0.011 0.002 TYR B 370 PHE 0.019 0.002 PHE A 355 TRP 0.017 0.001 TRP B 316 HIS 0.004 0.001 HIS B 494 Details of bonding type rmsd covalent geometry : bond 0.00424 (10304) covalent geometry : angle 0.55771 (13984) SS BOND : bond 0.00101 ( 2) SS BOND : angle 0.09646 ( 4) hydrogen bonds : bond 0.04227 ( 386) hydrogen bonds : angle 4.92605 ( 1068) *********************** 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 192 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 161 time to evaluate : 0.434 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: 0.7306 (m-30) cc_final: 0.7022 (p0) REVERT: A 291 LEU cc_start: 0.7080 (tt) cc_final: 0.6291 (mm) REVERT: A 402 LEU cc_start: 0.7297 (OUTLIER) cc_final: 0.6957 (mp) REVERT: A 425 VAL cc_start: 0.8110 (t) cc_final: 0.7784 (p) REVERT: B 275 ASP cc_start: 0.7220 (m-30) cc_final: 0.7017 (p0) REVERT: B 291 LEU cc_start: 0.7194 (tt) cc_final: 0.6491 (mm) REVERT: B 339 ASN cc_start: 0.7186 (m-40) cc_final: 0.6868 (m-40) REVERT: B 402 LEU cc_start: 0.7312 (OUTLIER) cc_final: 0.6914 (mp) REVERT: B 425 VAL cc_start: 0.8379 (p) cc_final: 0.7543 (p) REVERT: B 602 TYR cc_start: 0.6890 (m-80) cc_final: 0.6178 (m-10) REVERT: B 749 TYR cc_start: 0.7439 (m-80) cc_final: 0.7182 (m-80) outliers start: 31 outliers final: 8 residues processed: 184 average time/residue: 0.5220 time to fit residues: 103.7846 Evaluate side-chains 141 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 131 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 GLU 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 613 LEU 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 719 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 69 optimal weight: 0.7980 chunk 104 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 18 optimal weight: 8.9990 chunk 56 optimal weight: 5.9990 chunk 112 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 chunk 88 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 HIS ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 HIS ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 457 HIS B 634 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.153058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.120023 restraints weight = 13736.749| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.48 r_work: 0.3368 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 10306 Z= 0.252 Angle : 0.594 7.643 13988 Z= 0.319 Chirality : 0.046 0.150 1510 Planarity : 0.005 0.051 1758 Dihedral : 11.099 81.184 1400 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 4.44 % Allowed : 12.04 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.23), residues: 1192 helix: 0.09 (0.23), residues: 464 sheet: -0.57 (0.43), residues: 140 loop : -0.04 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 665 TYR 0.026 0.002 TYR A 723 PHE 0.022 0.002 PHE B 460 TRP 0.017 0.001 TRP B 316 HIS 0.005 0.001 HIS B 215 Details of bonding type rmsd covalent geometry : bond 0.00592 (10304) covalent geometry : angle 0.59430 (13984) SS BOND : bond 0.00095 ( 2) SS BOND : angle 0.56622 ( 4) hydrogen bonds : bond 0.04549 ( 386) hydrogen bonds : angle 4.95337 ( 1068) *********************** 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 182 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 134 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 MET cc_start: 0.7279 (mtt) cc_final: 0.6950 (mtm) REVERT: A 264 GLN cc_start: 0.6690 (OUTLIER) cc_final: 0.6356 (pm20) REVERT: A 275 ASP cc_start: 0.7353 (m-30) cc_final: 0.7062 (p0) REVERT: A 291 LEU cc_start: 0.7115 (tt) cc_final: 0.6364 (mm) REVERT: A 338 PHE cc_start: 0.6850 (OUTLIER) cc_final: 0.6392 (t80) REVERT: A 344 GLN cc_start: 0.7498 (OUTLIER) cc_final: 0.7274 (mm110) REVERT: A 402 LEU cc_start: 0.7280 (OUTLIER) cc_final: 0.6934 (mp) REVERT: B 220 TYR cc_start: 0.7646 (m-80) cc_final: 0.7395 (m-80) REVERT: B 264 GLN cc_start: 0.6632 (OUTLIER) cc_final: 0.6092 (pm20) REVERT: B 275 ASP cc_start: 0.7346 (m-30) cc_final: 0.7090 (p0) REVERT: B 291 LEU cc_start: 0.7368 (tt) cc_final: 0.6588 (mm) REVERT: B 339 ASN cc_start: 0.7123 (m-40) cc_final: 0.6713 (m-40) outliers start: 48 outliers final: 9 residues processed: 169 average time/residue: 0.4880 time to fit residues: 89.7090 Evaluate side-chains 130 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 GLN Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 344 GLN 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 613 LEU Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 264 GLN Chi-restraints excluded: chain B residue 354 CYS 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 1 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 66 optimal weight: 0.1980 chunk 14 optimal weight: 6.9990 chunk 91 optimal weight: 0.3980 chunk 92 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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** A 454 HIS B 264 GLN ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 345 ASN B 454 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.157623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.125191 restraints weight = 13825.063| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 2.49 r_work: 0.3440 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 10306 Z= 0.111 Angle : 0.506 10.380 13988 Z= 0.271 Chirality : 0.041 0.138 1510 Planarity : 0.003 0.027 1758 Dihedral : 10.698 78.578 1400 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.43 % Allowed : 13.80 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.24), residues: 1192 helix: 0.29 (0.23), residues: 476 sheet: -1.03 (0.41), residues: 160 loop : 0.36 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 665 TYR 0.025 0.001 TYR A 723 PHE 0.019 0.001 PHE A 744 TRP 0.024 0.001 TRP B 316 HIS 0.004 0.001 HIS B 163 Details of bonding type rmsd covalent geometry : bond 0.00255 (10304) covalent geometry : angle 0.50634 (13984) SS BOND : bond 0.00004 ( 2) SS BOND : angle 0.29694 ( 4) hydrogen bonds : bond 0.03420 ( 386) hydrogen bonds : angle 4.77022 ( 1068) *********************** 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: 37 poor density : 141 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 TYR cc_start: 0.7427 (m-80) cc_final: 0.7144 (m-80) REVERT: A 275 ASP cc_start: 0.7325 (m-30) cc_final: 0.7041 (p0) REVERT: A 291 LEU cc_start: 0.7210 (tt) cc_final: 0.6491 (mm) REVERT: A 402 LEU cc_start: 0.7200 (OUTLIER) cc_final: 0.6817 (mp) REVERT: A 602 TYR cc_start: 0.7221 (m-80) cc_final: 0.6972 (m-80) REVERT: A 738 MET cc_start: 0.8001 (ptt) cc_final: 0.7485 (ptt) REVERT: B 220 TYR cc_start: 0.7647 (m-80) cc_final: 0.7315 (m-80) REVERT: B 275 ASP cc_start: 0.7251 (m-30) cc_final: 0.7043 (p0) REVERT: B 291 LEU cc_start: 0.7386 (tt) cc_final: 0.6628 (mm) REVERT: B 339 ASN cc_start: 0.7121 (m-40) cc_final: 0.6749 (m-40) REVERT: B 619 MET cc_start: 0.7521 (OUTLIER) cc_final: 0.6769 (mpt) REVERT: B 736 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7892 (mt0) outliers start: 37 outliers final: 12 residues processed: 169 average time/residue: 0.4985 time to fit residues: 91.3868 Evaluate side-chains 142 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 THR 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 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 483 ASP Chi-restraints excluded: chain B residue 619 MET Chi-restraints excluded: chain B residue 667 CYS Chi-restraints excluded: chain B residue 736 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 30 optimal weight: 0.4980 chunk 32 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 115 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 67 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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 345 ASN ** 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 = 0.4054 r_free = 0.4054 target = 0.154426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.121637 restraints weight = 13888.274| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.51 r_work: 0.3413 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10306 Z= 0.193 Angle : 0.566 8.323 13988 Z= 0.299 Chirality : 0.043 0.143 1510 Planarity : 0.004 0.037 1758 Dihedral : 10.748 78.410 1400 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.61 % Allowed : 15.74 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.24), residues: 1192 helix: 0.26 (0.23), residues: 476 sheet: -1.25 (0.40), residues: 160 loop : 0.15 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 665 TYR 0.026 0.002 TYR B 723 PHE 0.019 0.002 PHE A 744 TRP 0.022 0.001 TRP B 316 HIS 0.004 0.001 HIS B 163 Details of bonding type rmsd covalent geometry : bond 0.00460 (10304) covalent geometry : angle 0.56556 (13984) SS BOND : bond 0.00041 ( 2) SS BOND : angle 0.50393 ( 4) hydrogen bonds : bond 0.03918 ( 386) hydrogen bonds : angle 4.77590 ( 1068) *********************** 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 171 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 132 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 MET cc_start: 0.7116 (OUTLIER) cc_final: 0.6913 (mtt) REVERT: A 275 ASP cc_start: 0.7361 (m-30) cc_final: 0.7077 (p0) REVERT: A 291 LEU cc_start: 0.7220 (tt) cc_final: 0.6484 (mm) REVERT: A 402 LEU cc_start: 0.7245 (OUTLIER) cc_final: 0.6879 (mp) REVERT: A 738 MET cc_start: 0.8162 (ptt) cc_final: 0.7583 (ptt) REVERT: B 220 TYR cc_start: 0.7687 (m-80) cc_final: 0.7344 (m-80) REVERT: B 275 ASP cc_start: 0.7319 (m-30) cc_final: 0.7090 (p0) REVERT: B 291 LEU cc_start: 0.7379 (tt) cc_final: 0.6670 (mm) REVERT: B 339 ASN cc_start: 0.7069 (m-40) cc_final: 0.6614 (m-40) REVERT: B 402 LEU cc_start: 0.7256 (OUTLIER) cc_final: 0.6914 (mp) REVERT: B 619 MET cc_start: 0.7538 (OUTLIER) cc_final: 0.6797 (mpt) REVERT: B 736 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7893 (mt0) outliers start: 39 outliers final: 15 residues processed: 161 average time/residue: 0.5245 time to fit residues: 91.3157 Evaluate side-chains 139 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 MET Chi-restraints excluded: chain A residue 249 THR 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 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 354 CYS 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 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 Chi-restraints excluded: chain B residue 736 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 7 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 83 optimal weight: 0.4980 chunk 18 optimal weight: 7.9990 chunk 23 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 53 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4051 r_free = 0.4051 target = 0.154589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.121782 restraints weight = 14110.109| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 2.54 r_work: 0.3431 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 10306 Z= 0.116 Angle : 0.515 9.563 13988 Z= 0.272 Chirality : 0.041 0.137 1510 Planarity : 0.003 0.035 1758 Dihedral : 10.491 76.659 1400 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.43 % Allowed : 16.67 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.24), residues: 1192 helix: 0.47 (0.23), residues: 476 sheet: -1.16 (0.40), residues: 160 loop : 0.25 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 665 TYR 0.029 0.001 TYR B 723 PHE 0.021 0.001 PHE A 744 TRP 0.026 0.001 TRP B 316 HIS 0.002 0.001 HIS A 705 Details of bonding type rmsd covalent geometry : bond 0.00275 (10304) covalent geometry : angle 0.51502 (13984) SS BOND : bond 0.00012 ( 2) SS BOND : angle 0.34472 ( 4) hydrogen bonds : bond 0.03331 ( 386) hydrogen bonds : angle 4.71255 ( 1068) *********************** 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 168 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 131 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 TYR cc_start: 0.7450 (m-80) cc_final: 0.7096 (m-80) REVERT: A 275 ASP cc_start: 0.7355 (m-30) cc_final: 0.7041 (p0) REVERT: A 291 LEU cc_start: 0.7190 (tt) cc_final: 0.6413 (mm) REVERT: A 402 LEU cc_start: 0.7160 (OUTLIER) cc_final: 0.6806 (mp) REVERT: A 738 MET cc_start: 0.8139 (ptt) cc_final: 0.7877 (ptt) REVERT: B 220 TYR cc_start: 0.7681 (m-80) cc_final: 0.7293 (m-80) REVERT: B 275 ASP cc_start: 0.7360 (m-30) cc_final: 0.7096 (p0) REVERT: B 291 LEU cc_start: 0.7337 (tt) cc_final: 0.6635 (mm) REVERT: B 327 MET cc_start: 0.4578 (OUTLIER) cc_final: 0.3284 (ttt) REVERT: B 619 MET cc_start: 0.7439 (OUTLIER) cc_final: 0.6682 (mpt) REVERT: B 736 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.7852 (mt0) outliers start: 37 outliers final: 10 residues processed: 156 average time/residue: 0.5075 time to fit residues: 85.8035 Evaluate side-chains 134 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 THR 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 667 CYS Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 327 MET Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 619 MET Chi-restraints excluded: chain B residue 667 CYS Chi-restraints excluded: chain B residue 736 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 99 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 chunk 53 optimal weight: 0.5980 chunk 15 optimal weight: 6.9990 chunk 14 optimal weight: 0.5980 chunk 78 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 87 optimal weight: 10.0000 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 ASN ** 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 = 0.4043 r_free = 0.4043 target = 0.153752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.120755 restraints weight = 13992.026| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.54 r_work: 0.3433 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10306 Z= 0.150 Angle : 0.553 10.373 13988 Z= 0.288 Chirality : 0.042 0.161 1510 Planarity : 0.004 0.054 1758 Dihedral : 10.506 76.843 1400 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.15 % Allowed : 17.78 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.24), residues: 1192 helix: 0.49 (0.23), residues: 476 sheet: -1.18 (0.40), residues: 160 loop : 0.24 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 740 TYR 0.024 0.001 TYR B 723 PHE 0.016 0.001 PHE A 460 TRP 0.026 0.001 TRP B 316 HIS 0.002 0.001 HIS B 215 Details of bonding type rmsd covalent geometry : bond 0.00358 (10304) covalent geometry : angle 0.55256 (13984) SS BOND : bond 0.00012 ( 2) SS BOND : angle 0.41866 ( 4) hydrogen bonds : bond 0.03580 ( 386) hydrogen bonds : angle 4.71779 ( 1068) *********************** 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 163 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 129 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 TYR cc_start: 0.7569 (m-80) cc_final: 0.7314 (m-80) REVERT: A 275 ASP cc_start: 0.7353 (m-30) cc_final: 0.7066 (p0) REVERT: A 291 LEU cc_start: 0.7213 (tt) cc_final: 0.6460 (mm) REVERT: A 402 LEU cc_start: 0.7276 (OUTLIER) cc_final: 0.6927 (mp) REVERT: A 407 TYR cc_start: 0.5821 (t80) cc_final: 0.5611 (t80) REVERT: A 602 TYR cc_start: 0.6987 (m-80) cc_final: 0.6400 (m-80) REVERT: A 619 MET cc_start: 0.7525 (OUTLIER) cc_final: 0.6720 (mpt) REVERT: A 738 MET cc_start: 0.8097 (ptt) cc_final: 0.7843 (ptt) REVERT: B 220 TYR cc_start: 0.7738 (m-80) cc_final: 0.7391 (m-80) REVERT: B 275 ASP cc_start: 0.7305 (m-30) cc_final: 0.7049 (p0) REVERT: B 291 LEU cc_start: 0.7354 (tt) cc_final: 0.6630 (mm) REVERT: B 402 LEU cc_start: 0.7279 (OUTLIER) cc_final: 0.6937 (mp) REVERT: B 407 TYR cc_start: 0.5974 (t80) cc_final: 0.5708 (t80) REVERT: B 602 TYR cc_start: 0.6995 (m-80) cc_final: 0.6379 (m-80) REVERT: B 619 MET cc_start: 0.7522 (OUTLIER) cc_final: 0.6682 (mpt) REVERT: B 736 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7807 (mt0) outliers start: 34 outliers final: 10 residues processed: 154 average time/residue: 0.5377 time to fit residues: 89.5302 Evaluate side-chains 137 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 0.393 ------------------------------------------------------------------------------- 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 483 ASP Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 619 MET Chi-restraints excluded: chain A residue 667 CYS 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 580 VAL Chi-restraints excluded: chain B residue 619 MET Chi-restraints excluded: chain B residue 667 CYS Chi-restraints excluded: chain B residue 736 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 41 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 chunk 115 optimal weight: 0.7980 chunk 99 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4078 r_free = 0.4078 target = 0.156436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.124571 restraints weight = 13744.436| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.44 r_work: 0.3451 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10306 Z= 0.130 Angle : 0.542 11.271 13988 Z= 0.283 Chirality : 0.041 0.152 1510 Planarity : 0.004 0.041 1758 Dihedral : 10.464 77.045 1400 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.24 % Allowed : 17.96 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.24), residues: 1192 helix: 0.52 (0.23), residues: 476 sheet: -1.18 (0.40), residues: 160 loop : 0.28 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 665 TYR 0.021 0.001 TYR B 723 PHE 0.026 0.001 PHE A 744 TRP 0.029 0.001 TRP B 316 HIS 0.002 0.001 HIS B 215 Details of bonding type rmsd covalent geometry : bond 0.00303 (10304) covalent geometry : angle 0.54198 (13984) SS BOND : bond 0.00009 ( 2) SS BOND : angle 0.38146 ( 4) hydrogen bonds : bond 0.03445 ( 386) hydrogen bonds : angle 4.67886 ( 1068) *********************** 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 168 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 133 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 TYR cc_start: 0.7581 (m-80) cc_final: 0.7302 (m-80) REVERT: A 275 ASP cc_start: 0.7337 (m-30) cc_final: 0.7036 (p0) REVERT: A 291 LEU cc_start: 0.7335 (tt) cc_final: 0.6646 (mm) REVERT: A 449 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7578 (mt-10) REVERT: A 602 TYR cc_start: 0.6987 (m-80) cc_final: 0.6659 (m-80) REVERT: A 738 MET cc_start: 0.8193 (ptt) cc_final: 0.7888 (ptt) REVERT: B 220 TYR cc_start: 0.7758 (m-80) cc_final: 0.7403 (m-80) REVERT: B 275 ASP cc_start: 0.7343 (m-30) cc_final: 0.7024 (p0) REVERT: B 291 LEU cc_start: 0.7404 (tt) cc_final: 0.6570 (mm) REVERT: B 402 LEU cc_start: 0.7180 (OUTLIER) cc_final: 0.6835 (mp) REVERT: B 602 TYR cc_start: 0.7017 (m-80) cc_final: 0.6612 (m-80) REVERT: B 736 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.7820 (mt0) outliers start: 35 outliers final: 12 residues processed: 158 average time/residue: 0.5298 time to fit residues: 90.4521 Evaluate side-chains 134 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.586 ------------------------------------------------------------------------------- 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 449 GLU Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 585 LEU 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 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 667 CYS Chi-restraints excluded: chain B residue 736 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 53 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 40 optimal weight: 0.3980 chunk 99 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 113 optimal weight: 0.5980 chunk 105 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 680 ASN ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4063 r_free = 0.4063 target = 0.155538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.122919 restraints weight = 14039.752| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.57 r_work: 0.3461 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3896 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= 0.114 Angle : 0.565 12.161 13988 Z= 0.291 Chirality : 0.041 0.149 1510 Planarity : 0.004 0.042 1758 Dihedral : 10.361 77.506 1400 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.76 % Allowed : 20.09 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.24), residues: 1192 helix: 0.52 (0.24), residues: 476 sheet: -0.77 (0.43), residues: 140 loop : 0.21 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 665 TYR 0.019 0.001 TYR B 723 PHE 0.015 0.001 PHE B 744 TRP 0.031 0.001 TRP B 316 HIS 0.002 0.001 HIS A 634 Details of bonding type rmsd covalent geometry : bond 0.00263 (10304) covalent geometry : angle 0.56482 (13984) SS BOND : bond 0.00006 ( 2) SS BOND : angle 0.25246 ( 4) hydrogen bonds : bond 0.03341 ( 386) hydrogen bonds : angle 4.74094 ( 1068) *********************** 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 151 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 220 TYR cc_start: 0.7511 (m-80) cc_final: 0.7266 (m-80) REVERT: A 275 ASP cc_start: 0.7316 (m-30) cc_final: 0.7031 (p0) REVERT: A 291 LEU cc_start: 0.7322 (tt) cc_final: 0.6685 (mm) REVERT: A 313 GLU cc_start: 0.6843 (mp0) cc_final: 0.5684 (tp30) REVERT: A 602 TYR cc_start: 0.6961 (m-80) cc_final: 0.6640 (m-80) REVERT: A 738 MET cc_start: 0.8146 (ptt) cc_final: 0.7888 (ptt) REVERT: B 220 TYR cc_start: 0.7757 (m-80) cc_final: 0.7392 (m-80) REVERT: B 275 ASP cc_start: 0.7317 (m-30) cc_final: 0.7012 (p0) REVERT: B 291 LEU cc_start: 0.7290 (tt) cc_final: 0.6580 (mm) REVERT: B 313 GLU cc_start: 0.6722 (mp0) cc_final: 0.5593 (tp30) REVERT: B 402 LEU cc_start: 0.7187 (OUTLIER) cc_final: 0.6836 (mp) REVERT: B 602 TYR cc_start: 0.7000 (m-80) cc_final: 0.6605 (m-80) REVERT: B 736 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7836 (mp10) outliers start: 19 outliers final: 10 residues processed: 148 average time/residue: 0.5078 time to fit residues: 81.5597 Evaluate side-chains 137 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 125 time to evaluate : 0.402 ------------------------------------------------------------------------------- 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 483 ASP Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 667 CYS 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 449 GLU Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 667 CYS Chi-restraints excluded: chain B residue 736 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 44 optimal weight: 0.9990 chunk 106 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 117 optimal weight: 0.6980 chunk 25 optimal weight: 0.0870 chunk 46 optimal weight: 8.9990 chunk 96 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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** ** 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 = 0.4073 r_free = 0.4073 target = 0.156530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.121224 restraints weight = 13912.774| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.78 r_work: 0.3493 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 10306 Z= 0.118 Angle : 0.567 12.616 13988 Z= 0.294 Chirality : 0.041 0.154 1510 Planarity : 0.004 0.043 1758 Dihedral : 10.330 76.976 1400 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.48 % Allowed : 20.83 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.25), residues: 1192 helix: 0.47 (0.24), residues: 482 sheet: -1.22 (0.41), residues: 160 loop : 0.28 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 448 TYR 0.018 0.001 TYR B 723 PHE 0.028 0.001 PHE A 744 TRP 0.034 0.001 TRP B 316 HIS 0.002 0.001 HIS B 163 Details of bonding type rmsd covalent geometry : bond 0.00279 (10304) covalent geometry : angle 0.56733 (13984) SS BOND : bond 0.00003 ( 2) SS BOND : angle 0.20848 ( 4) hydrogen bonds : bond 0.03313 ( 386) hydrogen bonds : angle 4.73343 ( 1068) ********************** 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 150 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 220 TYR cc_start: 0.7485 (m-80) cc_final: 0.7284 (m-80) REVERT: A 275 ASP cc_start: 0.7418 (m-30) cc_final: 0.7111 (p0) REVERT: A 291 LEU cc_start: 0.7301 (tt) cc_final: 0.6696 (mm) REVERT: A 338 PHE cc_start: 0.6733 (OUTLIER) cc_final: 0.6361 (t80) REVERT: A 602 TYR cc_start: 0.6948 (m-80) cc_final: 0.6576 (m-80) REVERT: B 220 TYR cc_start: 0.7716 (m-80) cc_final: 0.7371 (m-80) REVERT: B 275 ASP cc_start: 0.7412 (m-30) cc_final: 0.7076 (p0) REVERT: B 291 LEU cc_start: 0.7250 (tt) cc_final: 0.6535 (mm) REVERT: B 602 TYR cc_start: 0.6981 (m-80) cc_final: 0.6579 (m-80) REVERT: B 736 GLN cc_start: 0.8010 (OUTLIER) cc_final: 0.7718 (mp10) outliers start: 16 outliers final: 9 residues processed: 147 average time/residue: 0.5047 time to fit residues: 80.4186 Evaluate side-chains 138 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 354 CYS 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 B residue 354 CYS Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain B residue 667 CYS Chi-restraints excluded: chain B residue 736 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 92 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 84 optimal weight: 0.0670 chunk 38 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 99 optimal weight: 0.0870 chunk 77 optimal weight: 1.9990 overall best weight: 0.5896 ------------------------------------------------------------------------------- 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** ** 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 = 0.4083 r_free = 0.4083 target = 0.157452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.122511 restraints weight = 14066.766| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.73 r_work: 0.3467 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 10306 Z= 0.115 Angle : 0.575 12.591 13988 Z= 0.297 Chirality : 0.041 0.141 1510 Planarity : 0.004 0.042 1758 Dihedral : 10.248 76.757 1400 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.20 % Allowed : 21.57 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.25), residues: 1192 helix: 0.51 (0.24), residues: 482 sheet: -1.12 (0.42), residues: 156 loop : 0.20 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 448 TYR 0.012 0.001 TYR A 370 PHE 0.023 0.001 PHE A 460 TRP 0.035 0.001 TRP A 316 HIS 0.003 0.001 HIS B 163 Details of bonding type rmsd covalent geometry : bond 0.00272 (10304) covalent geometry : angle 0.57482 (13984) SS BOND : bond 0.00018 ( 2) SS BOND : angle 0.17305 ( 4) hydrogen bonds : bond 0.03306 ( 386) hydrogen bonds : angle 4.75511 ( 1068) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4124.54 seconds wall clock time: 70 minutes 53.41 seconds (4253.41 seconds total)