Starting phenix.real_space_refine on Sun Dec 29 07:54:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rwj_24717/12_2024/7rwj_24717.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rwj_24717/12_2024/7rwj_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_24717/12_2024/7rwj_24717.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rwj_24717/12_2024/7rwj_24717.map" model { file = "/net/cci-nas-00/data/ceres_data/7rwj_24717/12_2024/7rwj_24717.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rwj_24717/12_2024/7rwj_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 9.56, per 1000 atoms: 0.97 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: 2.77 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: 0.83 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: 2.71 Time building geometry restraints manager: 3.14 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: 0.00 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: 1.370 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: 0.410 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 27.480 Find NCS groups from input model: 0.260 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.500 ------------------------------------------------------------------------------- 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= 0.512 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 *********************** 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 : 0.993 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: 0.2845 time to fit residues: 54.6054 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 : 1.138 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 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= 0.228 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 *********************** 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 : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 175 GLU cc_start: 0.6841 (mt-10) cc_final: 0.6640 (mt-10) REVERT: B 224 ILE cc_start: 0.8796 (mm) cc_final: 0.8501 (mt) REVERT: B 500 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7781 (tm-30) REVERT: B 504 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7732 (pm20) REVERT: B 515 MET cc_start: 0.8122 (mmp) cc_final: 0.7856 (mmp) REVERT: B 647 ARG cc_start: 0.8449 (tmm160) cc_final: 0.8201 (tmm-80) REVERT: A 117 VAL cc_start: 0.8852 (t) cc_final: 0.8449 (p) REVERT: A 224 ILE cc_start: 0.8749 (mm) cc_final: 0.8445 (mt) REVERT: A 305 GLU cc_start: 0.7915 (tp30) cc_final: 0.7668 (tp30) REVERT: A 504 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7704 (pm20) REVERT: A 515 MET cc_start: 0.8139 (mmp) cc_final: 0.7875 (mmp) outliers start: 12 outliers final: 6 residues processed: 105 average time/residue: 0.2752 time to fit residues: 39.8803 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 : 1.114 ------------------------------------------------------------------------------- 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 60 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 90 optimal weight: 8.9990 chunk 74 optimal weight: 0.7980 chunk 30 optimal weight: 9.9990 chunk 109 optimal weight: 0.5980 chunk 117 optimal weight: 0.5980 chunk 97 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10156 Z= 0.262 Angle : 0.619 6.595 13786 Z= 0.318 Chirality : 0.043 0.193 1542 Planarity : 0.005 0.044 1714 Dihedral : 11.496 122.072 1440 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.55 % Favored : 95.29 % Rotamer: Outliers : 2.50 % Allowed : 13.01 % Favored : 84.49 % 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: 0.56 (0.18), residues: 808 sheet: -1.03 (0.92), residues: 28 loop : -1.88 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 155 HIS 0.004 0.001 HIS A 130 PHE 0.017 0.001 PHE A 61 TYR 0.016 0.001 TYR A 654 ARG 0.004 0.000 ARG A 153 *********************** 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 121 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 95 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 224 ILE cc_start: 0.8793 (mm) cc_final: 0.8501 (mt) REVERT: B 305 GLU cc_start: 0.7904 (tp30) cc_final: 0.7680 (tp30) REVERT: B 500 GLU cc_start: 0.8217 (tm-30) cc_final: 0.8016 (tm-30) REVERT: B 504 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7683 (pm20) REVERT: B 647 ARG cc_start: 0.8337 (tmm160) cc_final: 0.8095 (tmm-80) REVERT: A 175 GLU cc_start: 0.6830 (mt-10) cc_final: 0.6542 (mt-10) REVERT: A 224 ILE cc_start: 0.8766 (mm) cc_final: 0.8480 (mt) REVERT: A 504 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7687 (pm20) outliers start: 26 outliers final: 15 residues processed: 113 average time/residue: 0.2471 time to fit residues: 39.2081 Evaluate side-chains 107 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 1.187 ------------------------------------------------------------------------------- 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 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 107 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 56 optimal weight: 0.4980 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 73 optimal weight: 0.7980 chunk 109 optimal weight: 0.6980 chunk 115 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 103 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2071 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= 0.183 Angle : 0.555 6.421 13786 Z= 0.284 Chirality : 0.041 0.200 1542 Planarity : 0.004 0.039 1714 Dihedral : 10.397 129.929 1440 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.46 % Favored : 95.37 % Rotamer: Outliers : 2.70 % Allowed : 14.16 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.25), residues: 1188 helix: 1.02 (0.19), residues: 808 sheet: -0.79 (0.96), residues: 28 loop : -1.65 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 155 HIS 0.004 0.001 HIS A 130 PHE 0.015 0.001 PHE A 61 TYR 0.012 0.001 TYR A 654 ARG 0.003 0.000 ARG B 268 *********************** 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 126 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 98 time to evaluate : 1.177 Fit side-chains REVERT: B 175 GLU cc_start: 0.6696 (mt-10) cc_final: 0.6478 (mt-10) REVERT: B 224 ILE cc_start: 0.8725 (mm) cc_final: 0.8435 (mt) REVERT: B 305 GLU cc_start: 0.7917 (tp30) cc_final: 0.7657 (tp30) REVERT: B 504 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7669 (pm20) REVERT: B 647 ARG cc_start: 0.8241 (tmm160) cc_final: 0.8034 (tmm-80) REVERT: A 175 GLU cc_start: 0.6775 (mt-10) cc_final: 0.6500 (mt-10) REVERT: A 224 ILE cc_start: 0.8709 (mm) cc_final: 0.8372 (mt) REVERT: A 231 GLU cc_start: 0.8314 (tt0) cc_final: 0.8100 (mt-10) REVERT: A 504 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7678 (pm20) outliers start: 28 outliers final: 13 residues processed: 120 average time/residue: 0.2360 time to fit residues: 39.7731 Evaluate side-chains 100 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 1.134 ------------------------------------------------------------------------------- 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 504 GLU Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 595 HIS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 0.0040 chunk 65 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 104 optimal weight: 0.1980 chunk 29 optimal weight: 8.9990 overall best weight: 0.4992 ------------------------------------------------------------------------------- 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 A 370 ASN A 438 GLN A 518 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10156 Z= 0.163 Angle : 0.549 6.459 13786 Z= 0.282 Chirality : 0.041 0.256 1542 Planarity : 0.004 0.039 1714 Dihedral : 9.925 135.466 1440 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.46 % Favored : 95.37 % Rotamer: Outliers : 2.89 % Allowed : 14.74 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.26), residues: 1188 helix: 1.25 (0.19), residues: 810 sheet: -0.79 (0.77), residues: 40 loop : -1.61 (0.36), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 155 HIS 0.004 0.001 HIS B 130 PHE 0.015 0.001 PHE A 61 TYR 0.012 0.001 TYR B 589 ARG 0.004 0.000 ARG B 129 *********************** 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 122 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 92 time to evaluate : 1.252 Fit side-chains REVERT: B 175 GLU cc_start: 0.6694 (mt-10) cc_final: 0.6456 (mt-10) REVERT: B 224 ILE cc_start: 0.8704 (mm) cc_final: 0.8402 (mt) REVERT: B 504 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7595 (pm20) REVERT: B 707 MET cc_start: 0.7070 (tpt) cc_final: 0.6783 (tpt) REVERT: A 117 VAL cc_start: 0.8675 (t) cc_final: 0.8458 (p) REVERT: A 175 GLU cc_start: 0.6658 (mt-10) cc_final: 0.6379 (mt-10) REVERT: A 224 ILE cc_start: 0.8734 (mm) cc_final: 0.8408 (mt) REVERT: A 504 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7661 (pm20) outliers start: 30 outliers final: 20 residues processed: 116 average time/residue: 0.2379 time to fit residues: 39.0211 Evaluate side-chains 109 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 87 time to evaluate : 1.040 ------------------------------------------------------------------------------- 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 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 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 518 GLN 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 39 optimal weight: 0.9980 chunk 104 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 116 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 GLN B 518 GLN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2300 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= 0.228 Angle : 0.568 6.552 13786 Z= 0.292 Chirality : 0.043 0.240 1542 Planarity : 0.004 0.038 1714 Dihedral : 9.965 141.291 1440 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.21 % Favored : 95.62 % Rotamer: Outliers : 2.60 % Allowed : 14.64 % Favored : 82.76 % 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: 0.60 (0.26), residues: 1188 helix: 1.24 (0.19), residues: 810 sheet: -0.69 (0.96), residues: 28 loop : -1.50 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 155 HIS 0.004 0.001 HIS A 619 PHE 0.019 0.001 PHE A 22 TYR 0.011 0.001 TYR A 654 ARG 0.004 0.000 ARG B 268 *********************** 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 113 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 86 time to evaluate : 1.314 Fit side-chains REVERT: B 175 GLU cc_start: 0.6769 (mt-10) cc_final: 0.6487 (mt-10) REVERT: B 224 ILE cc_start: 0.8728 (mm) cc_final: 0.8443 (mt) REVERT: B 504 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7637 (pm20) REVERT: B 647 ARG cc_start: 0.8303 (tmm-80) cc_final: 0.7894 (ttp-170) REVERT: B 707 MET cc_start: 0.7135 (tpt) cc_final: 0.6896 (tpt) REVERT: A 117 VAL cc_start: 0.8663 (OUTLIER) cc_final: 0.8435 (p) REVERT: A 224 ILE cc_start: 0.8775 (mm) cc_final: 0.8500 (mt) REVERT: A 504 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7695 (pm20) outliers start: 27 outliers final: 18 residues processed: 107 average time/residue: 0.2521 time to fit residues: 38.2680 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 : 1.266 ------------------------------------------------------------------------------- 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 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 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 518 GLN 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 111 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 115 optimal weight: 0.0570 chunk 72 optimal weight: 0.0770 chunk 70 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 overall best weight: 0.5656 ------------------------------------------------------------------------------- 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 A 370 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10156 Z= 0.176 Angle : 0.549 6.567 13786 Z= 0.282 Chirality : 0.041 0.227 1542 Planarity : 0.004 0.037 1714 Dihedral : 9.814 144.505 1440 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.46 % Favored : 95.37 % Rotamer: Outliers : 2.79 % Allowed : 15.13 % Favored : 82.08 % 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: 0.72 (0.26), residues: 1188 helix: 1.33 (0.19), residues: 810 sheet: -0.57 (0.96), residues: 28 loop : -1.45 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 155 HIS 0.003 0.001 HIS A 130 PHE 0.020 0.001 PHE B 22 TYR 0.011 0.001 TYR B 589 ARG 0.003 0.000 ARG B 268 *********************** 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 118 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 89 time to evaluate : 1.050 Fit side-chains REVERT: B 175 GLU cc_start: 0.6700 (mt-10) cc_final: 0.6422 (mt-10) REVERT: B 224 ILE cc_start: 0.8741 (mm) cc_final: 0.8453 (mt) REVERT: B 504 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7627 (pm20) REVERT: B 515 MET cc_start: 0.8313 (mmp) cc_final: 0.7835 (mmp) REVERT: B 647 ARG cc_start: 0.8353 (tmm-80) cc_final: 0.7822 (ttp-170) REVERT: B 707 MET cc_start: 0.7199 (tpt) cc_final: 0.6995 (tpt) REVERT: A 117 VAL cc_start: 0.8630 (OUTLIER) cc_final: 0.8412 (p) REVERT: A 224 ILE cc_start: 0.8753 (mm) cc_final: 0.8475 (mt) REVERT: A 305 GLU cc_start: 0.8188 (tp30) cc_final: 0.7979 (tp30) REVERT: A 504 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7692 (pm20) REVERT: A 515 MET cc_start: 0.8319 (mmp) cc_final: 0.7824 (mmp) outliers start: 29 outliers final: 16 residues processed: 114 average time/residue: 0.2380 time to fit residues: 38.1267 Evaluate side-chains 103 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 1.170 ------------------------------------------------------------------------------- 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 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 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 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 71 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 10 optimal weight: 0.1980 chunk 90 optimal weight: 0.9980 chunk 105 optimal weight: 0.8980 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 539 ASN A 370 ASN A 518 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2388 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= 0.206 Angle : 0.562 6.603 13786 Z= 0.290 Chirality : 0.042 0.220 1542 Planarity : 0.004 0.038 1714 Dihedral : 9.815 150.324 1440 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.29 % Favored : 95.54 % 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: 0.74 (0.26), residues: 1188 helix: 1.35 (0.19), residues: 810 sheet: -0.66 (0.95), residues: 28 loop : -1.43 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 155 HIS 0.003 0.001 HIS A 130 PHE 0.021 0.001 PHE A 22 TYR 0.011 0.001 TYR B 589 ARG 0.003 0.000 ARG B 268 *********************** 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 121 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 90 time to evaluate : 1.703 Fit side-chains REVERT: B 175 GLU cc_start: 0.6670 (mt-10) cc_final: 0.6380 (mt-10) REVERT: B 224 ILE cc_start: 0.8740 (mm) cc_final: 0.8450 (mt) REVERT: B 305 GLU cc_start: 0.8162 (tp30) cc_final: 0.7934 (tp30) REVERT: B 504 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7647 (pm20) REVERT: B 515 MET cc_start: 0.8322 (mmp) cc_final: 0.8047 (mmt) REVERT: B 647 ARG cc_start: 0.8375 (tmm-80) cc_final: 0.7832 (ttp-170) REVERT: A 117 VAL cc_start: 0.8628 (OUTLIER) cc_final: 0.8404 (p) REVERT: A 224 ILE cc_start: 0.8734 (mm) cc_final: 0.8445 (mt) REVERT: A 504 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7705 (pm20) outliers start: 31 outliers final: 17 residues processed: 113 average time/residue: 0.2353 time to fit residues: 37.6736 Evaluate side-chains 107 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 1.266 ------------------------------------------------------------------------------- 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 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 323 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 97 optimal weight: 0.0040 chunk 70 optimal weight: 0.9990 chunk 113 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 overall best weight: 0.7392 ------------------------------------------------------------------------------- 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 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2469 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= 0.205 Angle : 0.570 6.615 13786 Z= 0.294 Chirality : 0.043 0.217 1542 Planarity : 0.004 0.037 1714 Dihedral : 9.872 168.218 1440 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.41 % Allowed : 16.38 % Favored : 81.21 % 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: 0.75 (0.26), residues: 1188 helix: 1.36 (0.19), residues: 814 sheet: -0.67 (0.95), residues: 28 loop : -1.48 (0.35), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 155 HIS 0.003 0.001 HIS A 619 PHE 0.022 0.001 PHE B 22 TYR 0.010 0.001 TYR B 589 ARG 0.003 0.000 ARG B 268 *********************** 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 112 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 87 time to evaluate : 1.129 Fit side-chains REVERT: B 224 ILE cc_start: 0.8729 (mm) cc_final: 0.8447 (mt) REVERT: B 305 GLU cc_start: 0.8147 (tp30) cc_final: 0.7939 (tp30) REVERT: B 504 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7620 (pm20) REVERT: B 647 ARG cc_start: 0.8446 (tmm-80) cc_final: 0.7847 (ttp-170) REVERT: A 117 VAL cc_start: 0.8608 (OUTLIER) cc_final: 0.8389 (p) REVERT: A 305 GLU cc_start: 0.8160 (tp30) cc_final: 0.7904 (tp30) REVERT: A 504 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7713 (pm20) outliers start: 25 outliers final: 17 residues processed: 106 average time/residue: 0.2417 time to fit residues: 36.1780 Evaluate side-chains 106 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 1.132 ------------------------------------------------------------------------------- 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 306 ILE Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 379 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 0.5980 chunk 79 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 73 optimal weight: 0.5980 chunk 58 optimal weight: 0.0470 chunk 75 optimal weight: 0.1980 chunk 101 optimal weight: 0.9980 chunk 29 optimal weight: 7.9990 overall best weight: 0.4478 ------------------------------------------------------------------------------- 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 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10156 Z= 0.156 Angle : 0.550 8.131 13786 Z= 0.281 Chirality : 0.041 0.210 1542 Planarity : 0.004 0.037 1714 Dihedral : 9.091 143.476 1440 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.83 % Allowed : 17.15 % Favored : 81.02 % 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: 1.01 (0.26), residues: 1188 helix: 1.55 (0.19), residues: 810 sheet: -0.52 (0.95), residues: 28 loop : -1.34 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 155 HIS 0.003 0.001 HIS A 130 PHE 0.022 0.001 PHE A 22 TYR 0.011 0.001 TYR B 589 ARG 0.003 0.000 ARG B 129 ********************** 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 108 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 1.183 Fit side-chains REVERT: B 504 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7608 (pm20) REVERT: B 601 GLU cc_start: 0.7408 (pm20) cc_final: 0.6653 (tt0) REVERT: B 647 ARG cc_start: 0.8421 (tmm-80) cc_final: 0.7833 (ttp-170) REVERT: A 601 GLU cc_start: 0.7714 (pm20) cc_final: 0.6587 (tt0) outliers start: 19 outliers final: 13 residues processed: 101 average time/residue: 0.2380 time to fit residues: 33.9677 Evaluate side-chains 101 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 1.638 ------------------------------------------------------------------------------- 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 323 ILE Chi-restraints excluded: chain B residue 328 VAL 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 243 VAL 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 508 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 5.9990 chunk 14 optimal weight: 0.0030 chunk 26 optimal weight: 0.7980 chunk 95 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 12 optimal weight: 0.3980 chunk 17 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 68 optimal weight: 0.0370 overall best weight: 0.4470 ------------------------------------------------------------------------------- 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 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN A 438 GLN A 539 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.143561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.124924 restraints weight = 14547.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.127804 restraints weight = 9016.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.129792 restraints weight = 6501.608| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10156 Z= 0.157 Angle : 0.552 8.435 13786 Z= 0.282 Chirality : 0.041 0.205 1542 Planarity : 0.004 0.037 1714 Dihedral : 8.754 131.135 1440 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.64 % Allowed : 17.44 % 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: 1.07 (0.25), residues: 1188 helix: 1.59 (0.19), residues: 814 sheet: -0.52 (0.94), residues: 28 loop : -1.34 (0.35), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 155 HIS 0.003 0.001 HIS A 130 PHE 0.023 0.001 PHE B 22 TYR 0.011 0.001 TYR B 589 ARG 0.004 0.000 ARG B 268 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1835.79 seconds wall clock time: 34 minutes 48.82 seconds (2088.82 seconds total)