Starting phenix.real_space_refine on Mon Jul 28 07:04:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rwj_24717/07_2025/7rwj_24717.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rwj_24717/07_2025/7rwj_24717.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rwj_24717/07_2025/7rwj_24717.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rwj_24717/07_2025/7rwj_24717.map" model { file = "/net/cci-nas-00/data/ceres_data/7rwj_24717/07_2025/7rwj_24717.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rwj_24717/07_2025/7rwj_24717.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.052 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 Ca 4 9.91 5 P 4 5.49 5 S 38 5.16 5 C 6486 2.51 5 N 1628 2.21 5 O 1746 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 9906 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4885 Classifications: {'peptide': 606} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 29, 'TRANS': 576} Chain breaks: 5 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 73 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 4, 'TYR:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 61 Chain: "A" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 68 Unusual residues: {' CA': 2, 'PGW': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PGW:plan-3': 2} Unresolved non-hydrogen planarities: 7 Restraints were copied for chains: B Time building chain proxies: 9.77, per 1000 atoms: 0.99 Number of scatterers: 9906 At special positions: 0 Unit cell: (127.2, 79.5, 98.58, 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) Ca 4 19.99 S 38 16.00 P 4 15.00 O 1746 8.00 N 1628 7.00 C 6486 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.49 Conformation dependent library (CDL) restraints added in 1.1 seconds 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 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: 54 helices and 2 sheets defined 69.3% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'B' and resid 28 through 45 removed outlier: 3.743A pdb=" N GLU B 42 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU B 43 " --> pdb=" O LEU B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 78 Processing helix chain 'B' and resid 79 through 86 removed outlier: 3.994A pdb=" N ASP B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 99 Processing helix chain 'B' and resid 103 through 117 removed outlier: 3.681A pdb=" N ARG B 107 " --> pdb=" O SER B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 155 Processing helix chain 'B' and resid 162 through 172 Processing helix chain 'B' and resid 174 through 189 removed outlier: 3.600A pdb=" N GLY B 178 " --> pdb=" O GLY B 174 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR B 180 " --> pdb=" O HIS B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 204 Processing helix chain 'B' and resid 209 through 238 Processing helix chain 'B' and resid 242 through 247 removed outlier: 3.699A pdb=" N HIS B 247 " --> pdb=" O SER B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 281 Processing helix chain 'B' and resid 282 through 311 Processing helix chain 'B' and resid 322 through 348 removed outlier: 3.624A pdb=" N ILE B 326 " --> pdb=" O PHE B 322 " (cutoff:3.500A) Proline residue: B 333 - end of helix Processing helix chain 'B' and resid 354 through 383 removed outlier: 3.609A pdb=" N TYR B 358 " --> pdb=" O THR B 354 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N VAL B 368 " --> pdb=" O GLN B 364 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N VAL B 369 " --> pdb=" O LYS B 365 " (cutoff:3.500A) Proline residue: B 377 - end of helix Processing helix chain 'B' and resid 388 through 392 Processing helix chain 'B' and resid 424 through 435 Processing helix chain 'B' and resid 435 through 447 Processing helix chain 'B' and resid 447 through 453 Processing helix chain 'B' and resid 492 through 501 removed outlier: 3.519A pdb=" N ARG B 498 " --> pdb=" O LEU B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 525 removed outlier: 4.283A pdb=" N ASP B 511 " --> pdb=" O ASP B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 553 removed outlier: 3.999A pdb=" N ARG B 545 " --> pdb=" O TRP B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 591 removed outlier: 3.805A pdb=" N ILE B 582 " --> pdb=" O TRP B 578 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N SER B 585 " --> pdb=" O SER B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 633 removed outlier: 3.846A pdb=" N LEU B 611 " --> pdb=" O CYS B 607 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU B 612 " --> pdb=" O TRP B 608 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR B 613 " --> pdb=" O ALA B 609 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE B 614 " --> pdb=" O LEU B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 644 Processing helix chain 'B' and resid 645 through 658 removed outlier: 4.284A pdb=" N ARG B 651 " --> pdb=" O ARG B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 724 removed outlier: 3.532A pdb=" N SER B 715 " --> pdb=" O GLY B 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 45 removed outlier: 3.743A pdb=" N GLU A 42 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 78 Processing helix chain 'A' and resid 79 through 86 removed outlier: 3.995A pdb=" N ASP A 83 " --> pdb=" O SER A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 99 Processing helix chain 'A' and resid 103 through 117 removed outlier: 3.682A pdb=" N ARG A 107 " --> pdb=" O SER A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 155 Processing helix chain 'A' and resid 162 through 172 Processing helix chain 'A' and resid 174 through 189 removed outlier: 3.600A pdb=" N GLY A 178 " --> pdb=" O GLY A 174 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR A 180 " --> pdb=" O HIS A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 204 Processing helix chain 'A' and resid 209 through 238 Processing helix chain 'A' and resid 242 through 247 removed outlier: 3.700A pdb=" N HIS A 247 " --> pdb=" O SER A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 281 Processing helix chain 'A' and resid 282 through 311 Processing helix chain 'A' and resid 322 through 348 removed outlier: 3.624A pdb=" N ILE A 326 " --> pdb=" O PHE A 322 " (cutoff:3.500A) Proline residue: A 333 - end of helix Processing helix chain 'A' and resid 354 through 383 removed outlier: 3.610A pdb=" N TYR A 358 " --> pdb=" O THR A 354 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N VAL A 368 " --> pdb=" O GLN A 364 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N VAL A 369 " --> pdb=" O LYS A 365 " (cutoff:3.500A) Proline residue: A 377 - end of helix Processing helix chain 'A' and resid 388 through 392 Processing helix chain 'A' and resid 424 through 435 Processing helix chain 'A' and resid 435 through 447 Processing helix chain 'A' and resid 447 through 453 Processing helix chain 'A' and resid 492 through 501 removed outlier: 3.519A pdb=" N ARG A 498 " --> pdb=" O LEU A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 525 removed outlier: 4.283A pdb=" N ASP A 511 " --> pdb=" O ASP A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 553 removed outlier: 3.999A pdb=" N ARG A 545 " --> pdb=" O TRP A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 591 removed outlier: 3.804A pdb=" N ILE A 582 " --> pdb=" O TRP A 578 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N SER A 585 " --> pdb=" O SER A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 633 removed outlier: 3.846A pdb=" N LEU A 611 " --> pdb=" O CYS A 607 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU A 612 " --> pdb=" O TRP A 608 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR A 613 " --> pdb=" O ALA A 609 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE A 614 " --> pdb=" O LEU A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 644 Processing helix chain 'A' and resid 645 through 658 removed outlier: 4.284A pdb=" N ARG A 651 " --> pdb=" O ARG A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 724 removed outlier: 3.532A pdb=" N SER A 715 " --> pdb=" O GLY A 711 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 48 through 52 Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 52 598 hydrogen bonds defined for protein. 1752 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: 2.66 Time building geometry restraints manager: 2.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 1530 1.27 - 1.41: 2725 1.41 - 1.54: 5691 1.54 - 1.67: 154 1.67 - 1.81: 56 Bond restraints: 10156 Sorted by residual: bond pdb=" C ILE B 605 " pdb=" O ILE B 605 " ideal model delta sigma weight residual 1.236 1.140 0.096 9.80e-03 1.04e+04 9.51e+01 bond pdb=" C ILE A 605 " pdb=" O ILE A 605 " ideal model delta sigma weight residual 1.236 1.140 0.096 9.80e-03 1.04e+04 9.51e+01 bond pdb=" C LEU A 380 " pdb=" O LEU A 380 " ideal model delta sigma weight residual 1.236 1.139 0.098 1.15e-02 7.56e+03 7.23e+01 bond pdb=" C LEU B 380 " pdb=" O LEU B 380 " ideal model delta sigma weight residual 1.236 1.139 0.097 1.15e-02 7.56e+03 7.11e+01 bond pdb=" C ILE B 379 " pdb=" O ILE B 379 " ideal model delta sigma weight residual 1.236 1.153 0.084 1.10e-02 8.26e+03 5.77e+01 ... (remaining 10151 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 13062 2.32 - 4.65: 566 4.65 - 6.97: 104 6.97 - 9.30: 40 9.30 - 11.62: 14 Bond angle restraints: 13786 Sorted by residual: angle pdb=" N PRO B 387 " pdb=" CA PRO B 387 " pdb=" C PRO B 387 " ideal model delta sigma weight residual 113.65 123.85 -10.20 1.35e+00 5.49e-01 5.71e+01 angle pdb=" N PRO A 387 " pdb=" CA PRO A 387 " pdb=" C PRO A 387 " ideal model delta sigma weight residual 113.65 123.85 -10.20 1.35e+00 5.49e-01 5.70e+01 angle pdb=" CA PHE A 383 " pdb=" CB PHE A 383 " pdb=" CG PHE A 383 " ideal model delta sigma weight residual 113.80 107.31 6.49 1.00e+00 1.00e+00 4.21e+01 angle pdb=" CA PHE B 383 " pdb=" CB PHE B 383 " pdb=" CG PHE B 383 " ideal model delta sigma weight residual 113.80 107.32 6.48 1.00e+00 1.00e+00 4.20e+01 angle pdb=" C PHE B 388 " pdb=" CA PHE B 388 " pdb=" CB PHE B 388 " ideal model delta sigma weight residual 114.52 103.43 11.09 1.81e+00 3.05e-01 3.75e+01 ... (remaining 13781 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.19: 5820 33.19 - 66.38: 168 66.38 - 99.58: 14 99.58 - 132.77: 4 132.77 - 165.96: 4 Dihedral angle restraints: 6010 sinusoidal: 2442 harmonic: 3568 Sorted by residual: dihedral pdb=" CA HIS B 130 " pdb=" C HIS B 130 " pdb=" N GLY B 131 " pdb=" CA GLY B 131 " ideal model delta harmonic sigma weight residual 180.00 -152.59 -27.41 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CA HIS A 130 " pdb=" C HIS A 130 " pdb=" N GLY A 131 " pdb=" CA GLY A 131 " ideal model delta harmonic sigma weight residual -180.00 -152.62 -27.38 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" C VAL A 386 " pdb=" N VAL A 386 " pdb=" CA VAL A 386 " pdb=" CB VAL A 386 " ideal model delta harmonic sigma weight residual -122.00 -135.03 13.03 0 2.50e+00 1.60e-01 2.71e+01 ... (remaining 6007 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 1392 0.103 - 0.205: 132 0.205 - 0.308: 10 0.308 - 0.410: 6 0.410 - 0.513: 2 Chirality restraints: 1542 Sorted by residual: chirality pdb=" CA ILE B 605 " pdb=" N ILE B 605 " pdb=" C ILE B 605 " pdb=" CB ILE B 605 " both_signs ideal model delta sigma weight residual False 2.43 2.95 -0.51 2.00e-01 2.50e+01 6.57e+00 chirality pdb=" CA ILE A 605 " pdb=" N ILE A 605 " pdb=" C ILE A 605 " pdb=" CB ILE A 605 " both_signs ideal model delta sigma weight residual False 2.43 2.95 -0.51 2.00e-01 2.50e+01 6.56e+00 chirality pdb=" CA PRO A 387 " pdb=" N PRO A 387 " pdb=" C PRO A 387 " pdb=" CB PRO A 387 " both_signs ideal model delta sigma weight residual False 2.72 2.31 0.40 2.00e-01 2.50e+01 4.10e+00 ... (remaining 1539 not shown) Planarity restraints: 1714 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 388 " 0.021 2.00e-02 2.50e+03 4.35e-02 1.89e+01 pdb=" C PHE B 388 " -0.075 2.00e-02 2.50e+03 pdb=" O PHE B 388 " 0.029 2.00e-02 2.50e+03 pdb=" N ALA B 389 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 388 " -0.021 2.00e-02 2.50e+03 4.31e-02 1.86e+01 pdb=" C PHE A 388 " 0.075 2.00e-02 2.50e+03 pdb=" O PHE A 388 " -0.028 2.00e-02 2.50e+03 pdb=" N ALA A 389 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 592 " -0.019 2.00e-02 2.50e+03 3.91e-02 1.53e+01 pdb=" C SER B 592 " 0.068 2.00e-02 2.50e+03 pdb=" O SER B 592 " -0.026 2.00e-02 2.50e+03 pdb=" N ASN B 593 " -0.023 2.00e-02 2.50e+03 ... (remaining 1711 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2356 2.79 - 3.31: 9114 3.31 - 3.84: 16595 3.84 - 4.37: 18859 4.37 - 4.90: 33428 Nonbonded interactions: 80352 Sorted by model distance: nonbonded pdb=" N GLU B 601 " pdb=" OE1 GLU B 601 " model vdw 2.258 3.120 nonbonded pdb=" N GLU A 601 " pdb=" OE1 GLU A 601 " model vdw 2.258 3.120 nonbonded pdb=" O CYS B 607 " pdb=" SG CYS B 607 " model vdw 2.260 3.400 nonbonded pdb=" O CYS A 607 " pdb=" SG CYS A 607 " model vdw 2.261 3.400 nonbonded pdb=" OH TYR A 180 " pdb=" OD2 ASP A 547 " model vdw 2.274 3.040 ... (remaining 80347 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.210 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: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 27.960 Find NCS groups from input model: 0.170 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 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 : 0.008 0.100 10156 Z= 0.495 Angle : 1.166 11.620 13786 Z= 0.666 Chirality : 0.068 0.513 1542 Planarity : 0.008 0.058 1714 Dihedral : 16.668 165.959 3690 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.05 % Favored : 94.61 % Rotamer: Outliers : 1.35 % Allowed : 6.74 % Favored : 91.91 % Cbeta Deviations : 0.34 % 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: -3.76 (0.20), residues: 1188 helix: -2.24 (0.14), residues: 802 sheet: -1.45 (0.81), residues: 40 loop : -2.79 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 227 HIS 0.008 0.002 HIS A 130 PHE 0.023 0.002 PHE B 367 TYR 0.027 0.002 TYR B 654 ARG 0.008 0.001 ARG A 250 Details of bonding type rmsd hydrogen bonds : bond 0.11862 ( 598) hydrogen bonds : angle 6.12802 ( 1752) covalent geometry : bond 0.00813 (10156) covalent geometry : angle 1.16608 (13786) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 117 VAL cc_start: 0.8809 (t) cc_final: 0.8600 (t) REVERT: B 121 GLU cc_start: 0.7116 (pp20) cc_final: 0.6798 (pt0) REVERT: B 281 LEU cc_start: 0.8182 (mt) cc_final: 0.7949 (tp) REVERT: B 515 MET cc_start: 0.7998 (mmp) cc_final: 0.7760 (mmt) REVERT: A 121 GLU cc_start: 0.7158 (pp20) cc_final: 0.6813 (pt0) REVERT: A 224 ILE cc_start: 0.8843 (mm) cc_final: 0.8562 (mt) REVERT: A 515 MET cc_start: 0.7948 (mmp) cc_final: 0.7714 (mmt) outliers start: 14 outliers final: 7 residues processed: 143 average time/residue: 0.2838 time to fit residues: 54.0880 Evaluate side-chains 95 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 395 TYR Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 395 TYR Chi-restraints excluded: chain A residue 605 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 0.7980 chunk 90 optimal weight: 7.9990 chunk 50 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 70 optimal weight: 0.5980 chunk 108 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 ASN B 171 ASN B 216 ASN B 230 GLN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 599 ASN A 148 ASN A 171 ASN A 216 ASN A 230 GLN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.142309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.123689 restraints weight = 14606.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.126488 restraints weight = 9090.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.128419 restraints weight = 6591.928| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10156 Z= 0.156 Angle : 0.621 6.920 13786 Z= 0.324 Chirality : 0.042 0.225 1542 Planarity : 0.005 0.044 1714 Dihedral : 12.767 152.663 1450 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.71 % Favored : 95.12 % Rotamer: Outliers : 1.16 % Allowed : 11.27 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.24), residues: 1188 helix: -0.24 (0.17), residues: 808 sheet: -1.19 (0.78), residues: 40 loop : -2.21 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 578 HIS 0.005 0.001 HIS B 130 PHE 0.015 0.001 PHE B 61 TYR 0.013 0.001 TYR B 589 ARG 0.005 0.000 ARG A 153 Details of bonding type rmsd hydrogen bonds : bond 0.04348 ( 598) hydrogen bonds : angle 4.44826 ( 1752) covalent geometry : bond 0.00355 (10156) covalent geometry : angle 0.62104 (13786) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 1.428 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 175 GLU cc_start: 0.6875 (mt-10) cc_final: 0.6656 (mt-10) REVERT: B 224 ILE cc_start: 0.8779 (mm) cc_final: 0.8474 (mt) REVERT: B 500 GLU cc_start: 0.8043 (tm-30) cc_final: 0.7780 (tm-30) REVERT: B 504 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7735 (pm20) REVERT: B 515 MET cc_start: 0.8095 (mmp) cc_final: 0.7843 (mmp) REVERT: B 647 ARG cc_start: 0.8464 (tmm160) cc_final: 0.8216 (tmm-80) REVERT: A 117 VAL cc_start: 0.8843 (t) cc_final: 0.8436 (p) REVERT: A 175 GLU cc_start: 0.6916 (mt-10) cc_final: 0.6703 (mt-10) REVERT: A 224 ILE cc_start: 0.8730 (mm) cc_final: 0.8414 (mt) REVERT: A 305 GLU cc_start: 0.7935 (tp30) cc_final: 0.7687 (tp30) REVERT: A 504 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7724 (pm20) REVERT: A 515 MET cc_start: 0.8121 (mmp) cc_final: 0.7867 (mmp) outliers start: 12 outliers final: 6 residues processed: 105 average time/residue: 0.3031 time to fit residues: 44.1494 Evaluate side-chains 96 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 2.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 504 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 90 optimal weight: 8.9990 chunk 107 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 51 optimal weight: 0.0770 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 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 = 0.3692 r_free = 0.3692 target = 0.139770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.120682 restraints weight = 14791.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.123489 restraints weight = 9228.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.125427 restraints weight = 6703.110| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 10156 Z= 0.198 Angle : 0.643 6.599 13786 Z= 0.331 Chirality : 0.044 0.195 1542 Planarity : 0.005 0.045 1714 Dihedral : 11.571 122.144 1440 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.80 % Favored : 95.03 % Rotamer: Outliers : 2.60 % Allowed : 13.39 % Favored : 84.01 % 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: -0.41 (0.25), residues: 1188 helix: 0.51 (0.18), residues: 806 sheet: -1.13 (0.92), residues: 28 loop : -1.95 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 155 HIS 0.004 0.002 HIS A 619 PHE 0.018 0.002 PHE A 61 TYR 0.017 0.001 TYR A 654 ARG 0.005 0.001 ARG A 153 Details of bonding type rmsd hydrogen bonds : bond 0.04537 ( 598) hydrogen bonds : angle 4.36246 ( 1752) covalent geometry : bond 0.00465 (10156) covalent geometry : angle 0.64299 (13786) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 224 ILE cc_start: 0.8793 (mm) cc_final: 0.8498 (mt) REVERT: B 305 GLU cc_start: 0.7925 (tp30) cc_final: 0.7699 (tp30) REVERT: B 500 GLU cc_start: 0.8253 (tm-30) cc_final: 0.8048 (tm-30) REVERT: B 504 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7709 (pm20) REVERT: B 647 ARG cc_start: 0.8384 (tmm160) cc_final: 0.8152 (tmm-80) REVERT: A 224 ILE cc_start: 0.8748 (mm) cc_final: 0.8462 (mt) REVERT: A 504 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7660 (pm20) outliers start: 27 outliers final: 16 residues processed: 115 average time/residue: 0.2533 time to fit residues: 40.9279 Evaluate side-chains 110 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 595 HIS Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 595 HIS Chi-restraints excluded: chain A residue 658 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 21 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 36 optimal weight: 0.4980 chunk 42 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.139714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.121091 restraints weight = 14627.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.123895 restraints weight = 9090.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.125839 restraints weight = 6575.078| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10156 Z= 0.157 Angle : 0.584 6.459 13786 Z= 0.300 Chirality : 0.042 0.199 1542 Planarity : 0.004 0.041 1714 Dihedral : 10.736 129.330 1440 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.63 % Favored : 95.20 % Rotamer: Outliers : 3.56 % Allowed : 13.97 % Favored : 82.47 % 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: 0.10 (0.25), residues: 1188 helix: 0.91 (0.19), residues: 804 sheet: -0.97 (0.97), residues: 28 loop : -1.77 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 155 HIS 0.004 0.001 HIS A 130 PHE 0.016 0.001 PHE A 61 TYR 0.012 0.001 TYR B 654 ARG 0.003 0.000 ARG B 268 Details of bonding type rmsd hydrogen bonds : bond 0.04187 ( 598) hydrogen bonds : angle 4.19657 ( 1752) covalent geometry : bond 0.00362 (10156) covalent geometry : angle 0.58434 (13786) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 93 time to evaluate : 1.205 Fit side-chains REVERT: B 22 PHE cc_start: 0.8482 (t80) cc_final: 0.8262 (t80) REVERT: B 224 ILE cc_start: 0.8761 (mm) cc_final: 0.8460 (mt) REVERT: B 447 ILE cc_start: 0.7855 (OUTLIER) cc_final: 0.7636 (pt) REVERT: B 504 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7769 (pm20) REVERT: B 647 ARG cc_start: 0.8324 (tmm160) cc_final: 0.8078 (tmm-80) REVERT: B 707 MET cc_start: 0.7264 (tpt) cc_final: 0.7061 (tpt) REVERT: A 224 ILE cc_start: 0.8709 (mm) cc_final: 0.8411 (mt) REVERT: A 231 GLU cc_start: 0.8351 (tt0) cc_final: 0.8118 (mt-10) REVERT: A 305 GLU cc_start: 0.8188 (tp30) cc_final: 0.7977 (tp30) REVERT: A 504 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7706 (pm20) outliers start: 37 outliers final: 21 residues processed: 118 average time/residue: 0.2629 time to fit residues: 44.1202 Evaluate side-chains 111 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 87 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 595 HIS Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 595 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 35 optimal weight: 0.7980 chunk 113 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.139885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.121229 restraints weight = 14665.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.124052 restraints weight = 9159.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.125911 restraints weight = 6629.078| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10156 Z= 0.150 Angle : 0.578 6.524 13786 Z= 0.297 Chirality : 0.043 0.266 1542 Planarity : 0.004 0.039 1714 Dihedral : 10.338 139.464 1440 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.63 % Favored : 95.20 % Rotamer: Outliers : 2.99 % Allowed : 15.32 % Favored : 81.70 % 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: 0.33 (0.25), residues: 1188 helix: 1.07 (0.19), residues: 806 sheet: -0.89 (0.96), residues: 28 loop : -1.64 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 155 HIS 0.004 0.001 HIS A 130 PHE 0.016 0.001 PHE A 61 TYR 0.012 0.001 TYR A 654 ARG 0.003 0.000 ARG B 647 Details of bonding type rmsd hydrogen bonds : bond 0.04115 ( 598) hydrogen bonds : angle 4.07940 ( 1752) covalent geometry : bond 0.00343 (10156) covalent geometry : angle 0.57838 (13786) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 94 time to evaluate : 1.055 Fit side-chains REVERT: B 224 ILE cc_start: 0.8730 (mm) cc_final: 0.8422 (mt) REVERT: B 447 ILE cc_start: 0.7842 (OUTLIER) cc_final: 0.7617 (pt) REVERT: B 504 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7683 (pm20) REVERT: A 117 VAL cc_start: 0.8696 (OUTLIER) cc_final: 0.8454 (p) REVERT: A 224 ILE cc_start: 0.8717 (mm) cc_final: 0.8430 (mt) REVERT: A 504 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7729 (pm20) outliers start: 31 outliers final: 18 residues processed: 115 average time/residue: 0.2232 time to fit residues: 36.2540 Evaluate side-chains 113 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 595 HIS Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 595 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 27 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 40 optimal weight: 7.9990 chunk 63 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 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 = 0.3685 r_free = 0.3685 target = 0.138554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.119785 restraints weight = 14785.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.122562 restraints weight = 9182.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.124445 restraints weight = 6668.470| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 10156 Z= 0.199 Angle : 0.623 6.605 13786 Z= 0.322 Chirality : 0.044 0.245 1542 Planarity : 0.005 0.048 1714 Dihedral : 10.569 154.362 1440 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.97 % Favored : 94.87 % Rotamer: Outliers : 3.28 % Allowed : 15.80 % Favored : 80.92 % 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: 0.21 (0.25), residues: 1188 helix: 0.98 (0.19), residues: 810 sheet: -0.99 (0.96), residues: 28 loop : -1.71 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 155 HIS 0.005 0.001 HIS A 619 PHE 0.018 0.002 PHE A 61 TYR 0.012 0.001 TYR A 654 ARG 0.005 0.000 ARG A 250 Details of bonding type rmsd hydrogen bonds : bond 0.04435 ( 598) hydrogen bonds : angle 4.16232 ( 1752) covalent geometry : bond 0.00469 (10156) covalent geometry : angle 0.62323 (13786) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 93 time to evaluate : 1.049 Fit side-chains REVERT: B 224 ILE cc_start: 0.8756 (mm) cc_final: 0.8443 (mt) REVERT: B 447 ILE cc_start: 0.7857 (OUTLIER) cc_final: 0.7617 (pt) REVERT: B 504 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7717 (pm20) REVERT: A 224 ILE cc_start: 0.8736 (mm) cc_final: 0.8425 (mt) REVERT: A 504 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7773 (pm20) outliers start: 34 outliers final: 22 residues processed: 115 average time/residue: 0.2424 time to fit residues: 38.8313 Evaluate side-chains 112 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 87 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 595 HIS Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 595 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 91 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 73 optimal weight: 0.4980 chunk 97 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 23 ASN A 370 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.140391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.121915 restraints weight = 14847.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.124760 restraints weight = 9098.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.126719 restraints weight = 6549.221| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10156 Z= 0.137 Angle : 0.571 6.610 13786 Z= 0.294 Chirality : 0.042 0.230 1542 Planarity : 0.004 0.041 1714 Dihedral : 10.246 176.154 1440 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.46 % Favored : 95.37 % Rotamer: Outliers : 2.79 % Allowed : 16.57 % Favored : 80.64 % 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 (0.26), residues: 1188 helix: 1.23 (0.19), residues: 806 sheet: -0.81 (0.95), residues: 28 loop : -1.54 (0.35), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 155 HIS 0.003 0.001 HIS B 130 PHE 0.015 0.001 PHE B 197 TYR 0.011 0.001 TYR B 589 ARG 0.003 0.000 ARG A 268 Details of bonding type rmsd hydrogen bonds : bond 0.04009 ( 598) hydrogen bonds : angle 4.00215 ( 1752) covalent geometry : bond 0.00308 (10156) covalent geometry : angle 0.57132 (13786) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 91 time to evaluate : 1.066 Fit side-chains REVERT: B 504 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7716 (pm20) REVERT: B 647 ARG cc_start: 0.8372 (tmm-80) cc_final: 0.7805 (ttp-170) REVERT: A 117 VAL cc_start: 0.8607 (OUTLIER) cc_final: 0.8383 (p) REVERT: A 224 ILE cc_start: 0.8702 (mm) cc_final: 0.8422 (mt) REVERT: A 504 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7739 (pm20) outliers start: 29 outliers final: 18 residues processed: 112 average time/residue: 0.2183 time to fit residues: 34.8662 Evaluate side-chains 107 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 595 HIS Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 595 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 116 optimal weight: 0.5980 chunk 109 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 52 optimal weight: 0.1980 chunk 22 optimal weight: 0.5980 chunk 102 optimal weight: 0.4980 chunk 48 optimal weight: 0.0980 chunk 107 optimal weight: 0.8980 chunk 110 optimal weight: 0.9980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.142981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.124287 restraints weight = 14788.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.127197 restraints weight = 9179.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.129102 restraints weight = 6615.591| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10156 Z= 0.109 Angle : 0.548 6.591 13786 Z= 0.281 Chirality : 0.041 0.222 1542 Planarity : 0.004 0.036 1714 Dihedral : 9.166 149.665 1440 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.46 % Favored : 95.45 % Rotamer: Outliers : 2.12 % Allowed : 17.44 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.26), residues: 1188 helix: 1.44 (0.19), residues: 808 sheet: -0.72 (0.93), residues: 28 loop : -1.41 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 155 HIS 0.004 0.001 HIS A 130 PHE 0.022 0.001 PHE A 22 TYR 0.012 0.001 TYR B 589 ARG 0.004 0.000 ARG A 129 Details of bonding type rmsd hydrogen bonds : bond 0.03711 ( 598) hydrogen bonds : angle 3.82740 ( 1752) covalent geometry : bond 0.00234 (10156) covalent geometry : angle 0.54758 (13786) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 1.159 Fit side-chains REVERT: B 305 GLU cc_start: 0.8133 (tp30) cc_final: 0.7909 (tp30) REVERT: B 504 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7654 (pm20) REVERT: B 647 ARG cc_start: 0.8390 (tmm-80) cc_final: 0.7849 (ttp-170) REVERT: A 224 ILE cc_start: 0.8706 (mm) cc_final: 0.8368 (mt) REVERT: A 305 GLU cc_start: 0.8198 (tp30) cc_final: 0.7883 (tp30) REVERT: A 601 GLU cc_start: 0.7760 (pm20) cc_final: 0.6659 (tt0) outliers start: 22 outliers final: 14 residues processed: 105 average time/residue: 0.2268 time to fit residues: 33.8240 Evaluate side-chains 104 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 595 HIS Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 595 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 94 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 117 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 GLN B 518 GLN ** B 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN A 438 GLN A 518 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.141345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.122717 restraints weight = 14830.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.125561 restraints weight = 9161.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.127525 restraints weight = 6605.929| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10156 Z= 0.139 Angle : 0.566 6.639 13786 Z= 0.291 Chirality : 0.042 0.213 1542 Planarity : 0.004 0.038 1714 Dihedral : 9.220 154.481 1440 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.31 % Allowed : 18.30 % Favored : 79.38 % 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: 0.86 (0.26), residues: 1188 helix: 1.45 (0.19), residues: 808 sheet: -0.81 (0.93), residues: 28 loop : -1.37 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 155 HIS 0.003 0.001 HIS A 130 PHE 0.021 0.001 PHE B 22 TYR 0.012 0.001 TYR A 187 ARG 0.003 0.000 ARG A 268 Details of bonding type rmsd hydrogen bonds : bond 0.03923 ( 598) hydrogen bonds : angle 3.89233 ( 1752) covalent geometry : bond 0.00316 (10156) covalent geometry : angle 0.56554 (13786) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 1.078 Fit side-chains REVERT: B 117 VAL cc_start: 0.8753 (t) cc_final: 0.8333 (m) REVERT: B 305 GLU cc_start: 0.8142 (tp30) cc_final: 0.7902 (tp30) REVERT: B 504 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7635 (pm20) REVERT: B 647 ARG cc_start: 0.8445 (tmm-80) cc_final: 0.7868 (ttp-170) REVERT: A 224 ILE cc_start: 0.8730 (mm) cc_final: 0.8450 (mt) REVERT: A 504 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7657 (pm20) REVERT: A 601 GLU cc_start: 0.7745 (pm20) cc_final: 0.6710 (tt0) outliers start: 24 outliers final: 19 residues processed: 108 average time/residue: 0.2404 time to fit residues: 36.7391 Evaluate side-chains 110 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 518 GLN Chi-restraints excluded: chain B residue 595 HIS Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 518 GLN Chi-restraints excluded: chain A residue 595 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 16 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 57 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 GLN ** B 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN A 518 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.141214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.122562 restraints weight = 14799.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.125463 restraints weight = 9181.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.127431 restraints weight = 6607.975| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10156 Z= 0.141 Angle : 0.577 7.542 13786 Z= 0.294 Chirality : 0.042 0.212 1542 Planarity : 0.004 0.037 1714 Dihedral : 9.278 163.335 1440 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.31 % Allowed : 18.79 % Favored : 78.90 % 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: 0.81 (0.25), residues: 1188 helix: 1.41 (0.19), residues: 812 sheet: -0.77 (0.93), residues: 28 loop : -1.43 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 155 HIS 0.003 0.001 HIS A 619 PHE 0.022 0.001 PHE A 22 TYR 0.011 0.001 TYR B 589 ARG 0.003 0.000 ARG A 129 Details of bonding type rmsd hydrogen bonds : bond 0.03952 ( 598) hydrogen bonds : angle 3.89583 ( 1752) covalent geometry : bond 0.00323 (10156) covalent geometry : angle 0.57681 (13786) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 89 time to evaluate : 1.164 Fit side-chains REVERT: B 117 VAL cc_start: 0.8752 (t) cc_final: 0.8336 (m) REVERT: B 504 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7637 (pm20) REVERT: B 647 ARG cc_start: 0.8453 (tmm-80) cc_final: 0.7845 (ttp-170) REVERT: A 224 ILE cc_start: 0.8737 (mm) cc_final: 0.8453 (mt) REVERT: A 305 GLU cc_start: 0.8180 (tp30) cc_final: 0.7924 (tp30) REVERT: A 504 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7675 (pm20) REVERT: A 601 GLU cc_start: 0.7740 (pm20) cc_final: 0.6691 (tt0) outliers start: 24 outliers final: 20 residues processed: 107 average time/residue: 0.3094 time to fit residues: 49.8977 Evaluate side-chains 110 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 1.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 518 GLN Chi-restraints excluded: chain B residue 595 HIS Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 518 GLN Chi-restraints excluded: chain A residue 595 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 91 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 48 optimal weight: 0.0060 chunk 88 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 chunk 112 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 GLN ** B 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN A 518 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.140943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.122435 restraints weight = 14800.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.125303 restraints weight = 9114.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.127272 restraints weight = 6540.653| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10156 Z= 0.140 Angle : 0.576 7.528 13786 Z= 0.294 Chirality : 0.042 0.209 1542 Planarity : 0.004 0.037 1714 Dihedral : 9.301 173.361 1440 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.50 % Allowed : 18.59 % Favored : 78.90 % 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: 0.83 (0.25), residues: 1188 helix: 1.41 (0.19), residues: 812 sheet: -0.74 (0.94), residues: 28 loop : -1.40 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 155 HIS 0.003 0.001 HIS A 619 PHE 0.022 0.001 PHE B 22 TYR 0.011 0.001 TYR B 589 ARG 0.004 0.000 ARG A 129 Details of bonding type rmsd hydrogen bonds : bond 0.03960 ( 598) hydrogen bonds : angle 3.88826 ( 1752) covalent geometry : bond 0.00319 (10156) covalent geometry : angle 0.57567 (13786) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2891.92 seconds wall clock time: 52 minutes 52.56 seconds (3172.56 seconds total)