Starting phenix.real_space_refine on Wed Mar 4 02:21:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rwj_24717/03_2026/7rwj_24717.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rwj_24717/03_2026/7rwj_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_24717/03_2026/7rwj_24717.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rwj_24717/03_2026/7rwj_24717.map" model { file = "/net/cci-nas-00/data/ceres_data/7rwj_24717/03_2026/7rwj_24717.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rwj_24717/03_2026/7rwj_24717.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9906 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" 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: {'GLU:plan': 6, 'ASP:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 4, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 61 Chain: "B" 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: A Time building chain proxies: 3.82, per 1000 atoms: 0.39 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: 0.58 Conformation dependent library (CDL) restraints added in 496.3 milliseconds 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: 0.21 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: 1.44 Time building geometry restraints manager: 0.83 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: 0.01 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' } 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: 2.010 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.890 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.630 ------------------------------------------------------------------------------- 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 : 9.27 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.008 0.001 ARG A 250 TYR 0.027 0.002 TYR B 654 PHE 0.023 0.002 PHE B 367 TRP 0.029 0.002 TRP B 227 HIS 0.008 0.002 HIS A 130 Details of bonding type rmsd covalent geometry : bond 0.00813 (10156) covalent geometry : angle 1.16608 (13786) hydrogen bonds : bond 0.11862 ( 598) hydrogen bonds : angle 6.12802 ( 1752) *********************** 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 : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 117 VAL cc_start: 0.8809 (t) cc_final: 0.8601 (t) REVERT: B 121 GLU cc_start: 0.7116 (pp20) cc_final: 0.6800 (pt0) REVERT: B 281 LEU cc_start: 0.8182 (mt) cc_final: 0.7950 (tp) REVERT: B 515 MET cc_start: 0.7995 (mmp) cc_final: 0.7760 (mmt) REVERT: A 121 GLU cc_start: 0.7158 (pp20) cc_final: 0.6814 (pt0) REVERT: A 224 ILE cc_start: 0.8843 (mm) cc_final: 0.8563 (mt) REVERT: A 515 MET cc_start: 0.7949 (mmp) cc_final: 0.7714 (mmt) outliers start: 14 outliers final: 7 residues processed: 143 average time/residue: 0.1241 time to fit residues: 23.3993 Evaluate side-chains 92 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.342 ------------------------------------------------------------------------------- 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 108 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 117 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 499 ASN 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 A 599 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.142945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.124417 restraints weight = 14604.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.127216 restraints weight = 9090.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.129168 restraints weight = 6575.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.130527 restraints weight = 5219.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.131419 restraints weight = 4413.078| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10156 Z= 0.144 Angle : 0.613 6.992 13786 Z= 0.319 Chirality : 0.042 0.227 1542 Planarity : 0.005 0.044 1714 Dihedral : 12.750 153.022 1450 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.46 % Favored : 95.37 % Rotamer: Outliers : 1.35 % Allowed : 10.79 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.24), residues: 1188 helix: -0.22 (0.17), residues: 808 sheet: -1.16 (0.78), residues: 40 loop : -2.21 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 644 TYR 0.013 0.001 TYR B 589 PHE 0.014 0.001 PHE B 61 TRP 0.026 0.002 TRP B 578 HIS 0.005 0.001 HIS A 130 Details of bonding type rmsd covalent geometry : bond 0.00324 (10156) covalent geometry : angle 0.61276 (13786) hydrogen bonds : bond 0.04270 ( 598) hydrogen bonds : angle 4.42170 ( 1752) *********************** 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 110 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 175 GLU cc_start: 0.6847 (mt-10) cc_final: 0.6620 (mt-10) REVERT: B 224 ILE cc_start: 0.8769 (mm) cc_final: 0.8451 (mt) REVERT: B 500 GLU cc_start: 0.7959 (tm-30) cc_final: 0.7732 (tm-30) REVERT: B 504 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7704 (pm20) REVERT: B 515 MET cc_start: 0.8066 (mmp) cc_final: 0.7831 (mmp) REVERT: B 647 ARG cc_start: 0.8453 (tmm160) cc_final: 0.8219 (tmm-80) REVERT: A 117 VAL cc_start: 0.8850 (t) cc_final: 0.8425 (p) REVERT: A 175 GLU cc_start: 0.6904 (mt-10) cc_final: 0.6685 (mt-10) REVERT: A 224 ILE cc_start: 0.8720 (mm) cc_final: 0.8400 (mt) REVERT: A 305 GLU cc_start: 0.7911 (tp30) cc_final: 0.7671 (tp30) REVERT: A 504 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7702 (pm20) REVERT: A 515 MET cc_start: 0.8086 (mmp) cc_final: 0.7854 (mmp) outliers start: 14 outliers final: 6 residues processed: 106 average time/residue: 0.1078 time to fit residues: 15.7522 Evaluate side-chains 95 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.334 ------------------------------------------------------------------------------- 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 37 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 72 optimal weight: 0.4980 chunk 84 optimal weight: 0.0040 chunk 108 optimal weight: 0.0970 chunk 102 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 49 optimal weight: 0.2980 chunk 58 optimal weight: 5.9990 overall best weight: 0.3190 ------------------------------------------------------------------------------- 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 499 ASN A 370 ASN A 499 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.144915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.126444 restraints weight = 14557.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.129394 restraints weight = 8918.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.131395 restraints weight = 6349.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.132791 restraints weight = 5009.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.133538 restraints weight = 4204.878| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10156 Z= 0.104 Angle : 0.546 6.528 13786 Z= 0.278 Chirality : 0.040 0.192 1542 Planarity : 0.004 0.040 1714 Dihedral : 11.171 133.983 1440 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.63 % Favored : 95.20 % Rotamer: Outliers : 2.12 % Allowed : 11.85 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.25), residues: 1188 helix: 0.84 (0.18), residues: 796 sheet: -0.89 (0.77), residues: 40 loop : -1.82 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 153 TYR 0.012 0.001 TYR A 589 PHE 0.014 0.001 PHE A 61 TRP 0.017 0.002 TRP B 155 HIS 0.004 0.001 HIS A 130 Details of bonding type rmsd covalent geometry : bond 0.00214 (10156) covalent geometry : angle 0.54551 (13786) hydrogen bonds : bond 0.03701 ( 598) hydrogen bonds : angle 4.03591 ( 1752) *********************** 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 119 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 224 ILE cc_start: 0.8703 (mm) cc_final: 0.8412 (mt) REVERT: B 231 GLU cc_start: 0.8165 (tt0) cc_final: 0.7915 (mt-10) REVERT: B 504 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7610 (pm20) REVERT: B 515 MET cc_start: 0.8122 (mmp) cc_final: 0.7887 (mmp) REVERT: B 649 MET cc_start: 0.8302 (mmm) cc_final: 0.8009 (mmm) REVERT: A 117 VAL cc_start: 0.8752 (t) cc_final: 0.8491 (p) REVERT: A 224 ILE cc_start: 0.8658 (mm) cc_final: 0.8315 (mt) REVERT: A 515 MET cc_start: 0.8062 (mmp) cc_final: 0.7830 (mmp) outliers start: 22 outliers final: 13 residues processed: 115 average time/residue: 0.1019 time to fit residues: 16.3802 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 : 0.234 ------------------------------------------------------------------------------- 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 499 ASN Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 508 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 396 LEU Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 508 VAL 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 25 optimal weight: 0.8980 chunk 58 optimal weight: 0.2980 chunk 88 optimal weight: 0.6980 chunk 112 optimal weight: 0.0000 chunk 78 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 52 optimal weight: 0.0370 chunk 24 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 overall best weight: 0.3862 ------------------------------------------------------------------------------- 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 499 ASN B 518 GLN A 370 ASN A 438 GLN ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.145398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.126734 restraints weight = 14679.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.129613 restraints weight = 9110.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.131406 restraints weight = 6569.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.132896 restraints weight = 5268.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.133809 restraints weight = 4434.410| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2068 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= 0.106 Angle : 0.532 6.537 13786 Z= 0.272 Chirality : 0.040 0.191 1542 Planarity : 0.004 0.040 1714 Dihedral : 10.605 124.480 1440 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.38 % Favored : 95.45 % Rotamer: Outliers : 2.41 % Allowed : 12.43 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.26), residues: 1188 helix: 1.16 (0.19), residues: 812 sheet: -0.73 (0.77), residues: 40 loop : -1.74 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 268 TYR 0.019 0.001 TYR B 589 PHE 0.015 0.001 PHE A 61 TRP 0.018 0.001 TRP A 155 HIS 0.003 0.001 HIS B 130 Details of bonding type rmsd covalent geometry : bond 0.00224 (10156) covalent geometry : angle 0.53174 (13786) hydrogen bonds : bond 0.03651 ( 598) hydrogen bonds : angle 3.93770 ( 1752) *********************** 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 119 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 0.277 Fit side-chains REVERT: B 224 ILE cc_start: 0.8692 (mm) cc_final: 0.8374 (mt) REVERT: B 231 GLU cc_start: 0.8190 (tt0) cc_final: 0.7907 (mt-10) REVERT: B 504 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7546 (pm20) REVERT: B 647 ARG cc_start: 0.8204 (tmm-80) cc_final: 0.7824 (ttp-170) REVERT: B 649 MET cc_start: 0.8334 (mmm) cc_final: 0.8071 (mmm) REVERT: A 117 VAL cc_start: 0.8695 (t) cc_final: 0.8448 (p) REVERT: A 224 ILE cc_start: 0.8697 (mm) cc_final: 0.8331 (mt) outliers start: 25 outliers final: 13 residues processed: 114 average time/residue: 0.0916 time to fit residues: 14.8026 Evaluate side-chains 102 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.351 ------------------------------------------------------------------------------- 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 499 ASN 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 328 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 658 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 117 optimal weight: 0.9990 chunk 104 optimal weight: 0.5980 chunk 97 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- 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 499 ASN A 370 ASN A 499 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.141660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.122999 restraints weight = 14655.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.125940 restraints weight = 9064.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.127911 restraints weight = 6502.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.129125 restraints weight = 5140.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.130189 restraints weight = 4382.668| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.2151 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= 0.153 Angle : 0.566 6.533 13786 Z= 0.292 Chirality : 0.042 0.200 1542 Planarity : 0.004 0.039 1714 Dihedral : 10.321 132.410 1440 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.38 % Favored : 95.45 % Rotamer: Outliers : 2.70 % Allowed : 13.20 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.26), residues: 1188 helix: 1.18 (0.19), residues: 812 sheet: -0.73 (0.78), residues: 40 loop : -1.67 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 498 TYR 0.015 0.001 TYR B 589 PHE 0.017 0.001 PHE A 61 TRP 0.021 0.001 TRP A 155 HIS 0.004 0.001 HIS B 619 Details of bonding type rmsd covalent geometry : bond 0.00352 (10156) covalent geometry : angle 0.56594 (13786) hydrogen bonds : bond 0.03981 ( 598) hydrogen bonds : angle 3.93963 ( 1752) *********************** 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 120 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 92 time to evaluate : 0.249 Fit side-chains REVERT: B 224 ILE cc_start: 0.8713 (mm) cc_final: 0.8394 (mt) REVERT: B 305 GLU cc_start: 0.8221 (tp30) cc_final: 0.7994 (tp30) REVERT: B 504 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7566 (pm20) REVERT: B 647 ARG cc_start: 0.8359 (tmm-80) cc_final: 0.7860 (ttp-170) REVERT: A 117 VAL cc_start: 0.8746 (t) cc_final: 0.8486 (p) REVERT: A 224 ILE cc_start: 0.8714 (mm) cc_final: 0.8435 (mt) REVERT: A 504 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7661 (pm20) outliers start: 28 outliers final: 16 residues processed: 115 average time/residue: 0.0933 time to fit residues: 15.0245 Evaluate side-chains 107 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 0.336 ------------------------------------------------------------------------------- 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 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 499 ASN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 47 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 85 optimal weight: 0.4980 chunk 89 optimal weight: 7.9990 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** B 499 ASN A 370 ASN A 499 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.142071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.123419 restraints weight = 14644.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.126316 restraints weight = 9074.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.128279 restraints weight = 6526.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.129649 restraints weight = 5177.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.130534 restraints weight = 4365.810| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2233 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= 0.136 Angle : 0.552 6.542 13786 Z= 0.284 Chirality : 0.041 0.204 1542 Planarity : 0.004 0.037 1714 Dihedral : 10.058 138.657 1440 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.55 % Favored : 95.29 % Rotamer: Outliers : 2.60 % Allowed : 14.07 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.25), residues: 1188 helix: 1.27 (0.19), residues: 812 sheet: -0.58 (0.97), residues: 28 loop : -1.57 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 647 TYR 0.014 0.001 TYR B 589 PHE 0.019 0.001 PHE B 22 TRP 0.025 0.001 TRP A 155 HIS 0.003 0.001 HIS A 130 Details of bonding type rmsd covalent geometry : bond 0.00305 (10156) covalent geometry : angle 0.55203 (13786) hydrogen bonds : bond 0.03897 ( 598) hydrogen bonds : angle 3.89460 ( 1752) *********************** 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 115 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 88 time to evaluate : 0.338 Fit side-chains REVERT: B 224 ILE cc_start: 0.8709 (mm) cc_final: 0.8426 (mt) REVERT: B 504 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7544 (pm20) REVERT: B 647 ARG cc_start: 0.8395 (tmm-80) cc_final: 0.7727 (ttp-170) REVERT: A 117 VAL cc_start: 0.8676 (t) cc_final: 0.8420 (p) REVERT: A 224 ILE cc_start: 0.8709 (mm) cc_final: 0.8353 (mt) outliers start: 27 outliers final: 19 residues processed: 110 average time/residue: 0.0976 time to fit residues: 15.1021 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 : 0.367 ------------------------------------------------------------------------------- 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 306 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 499 ASN 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 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 499 ASN 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 27 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 93 optimal weight: 0.0040 chunk 8 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 67 optimal weight: 0.6980 overall best weight: 0.6192 ------------------------------------------------------------------------------- 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 499 ASN A 370 ASN A 499 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.142497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.123677 restraints weight = 14657.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.126579 restraints weight = 9142.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.128553 restraints weight = 6603.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.129932 restraints weight = 5247.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.130862 restraints weight = 4441.507| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10156 Z= 0.128 Angle : 0.552 6.579 13786 Z= 0.284 Chirality : 0.042 0.268 1542 Planarity : 0.004 0.061 1714 Dihedral : 9.906 142.567 1440 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.46 % Favored : 95.37 % Rotamer: Outliers : 2.89 % Allowed : 14.35 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.25), residues: 1188 helix: 1.35 (0.19), residues: 812 sheet: -0.64 (0.96), residues: 28 loop : -1.51 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 498 TYR 0.014 0.001 TYR B 589 PHE 0.015 0.001 PHE A 61 TRP 0.027 0.001 TRP A 155 HIS 0.006 0.001 HIS A 130 Details of bonding type rmsd covalent geometry : bond 0.00286 (10156) covalent geometry : angle 0.55210 (13786) hydrogen bonds : bond 0.03846 ( 598) hydrogen bonds : angle 3.85081 ( 1752) *********************** 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 119 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 89 time to evaluate : 0.348 Fit side-chains REVERT: B 224 ILE cc_start: 0.8696 (mm) cc_final: 0.8421 (mt) REVERT: B 504 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7589 (pm20) REVERT: B 647 ARG cc_start: 0.8420 (tmm-80) cc_final: 0.7746 (ttp-170) REVERT: A 117 VAL cc_start: 0.8637 (t) cc_final: 0.8386 (p) REVERT: A 224 ILE cc_start: 0.8697 (mm) cc_final: 0.8338 (mt) REVERT: A 504 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7676 (pm20) outliers start: 30 outliers final: 19 residues processed: 116 average time/residue: 0.0985 time to fit residues: 16.0424 Evaluate side-chains 109 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 0.318 ------------------------------------------------------------------------------- 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 499 ASN 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 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 499 ASN 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 83 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 115 optimal weight: 0.0010 chunk 16 optimal weight: 0.8980 overall best weight: 0.5786 ------------------------------------------------------------------------------- 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 499 ASN A 370 ASN ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.142513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.123812 restraints weight = 14592.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.126721 restraints weight = 9070.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.128689 restraints weight = 6525.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.130019 restraints weight = 5179.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.130850 restraints weight = 4385.943| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2352 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= 0.123 Angle : 0.548 6.601 13786 Z= 0.282 Chirality : 0.042 0.259 1542 Planarity : 0.004 0.055 1714 Dihedral : 9.767 146.786 1440 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.55 % Favored : 95.29 % Rotamer: Outliers : 2.50 % Allowed : 15.22 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.26), residues: 1188 helix: 1.43 (0.19), residues: 812 sheet: -0.65 (0.95), residues: 28 loop : -1.47 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 268 TYR 0.014 0.001 TYR B 589 PHE 0.021 0.001 PHE A 22 TRP 0.029 0.001 TRP A 155 HIS 0.003 0.001 HIS B 130 Details of bonding type rmsd covalent geometry : bond 0.00274 (10156) covalent geometry : angle 0.54831 (13786) hydrogen bonds : bond 0.03810 ( 598) hydrogen bonds : angle 3.82628 ( 1752) *********************** 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 117 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 91 time to evaluate : 0.335 Fit side-chains REVERT: B 224 ILE cc_start: 0.8705 (mm) cc_final: 0.8406 (mt) REVERT: B 305 GLU cc_start: 0.8154 (tp30) cc_final: 0.7918 (tp30) REVERT: B 504 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7548 (pm20) REVERT: A 117 VAL cc_start: 0.8612 (t) cc_final: 0.8361 (p) REVERT: A 224 ILE cc_start: 0.8696 (mm) cc_final: 0.8338 (mt) REVERT: A 305 GLU cc_start: 0.8155 (tp30) cc_final: 0.7901 (tp30) REVERT: A 504 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7674 (pm20) outliers start: 26 outliers final: 18 residues processed: 112 average time/residue: 0.1052 time to fit residues: 16.4536 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 : 0.349 ------------------------------------------------------------------------------- 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 499 ASN 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 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 499 ASN 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 12 optimal weight: 2.9990 chunk 10 optimal weight: 0.4980 chunk 20 optimal weight: 0.9990 chunk 99 optimal weight: 0.5980 chunk 73 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 113 optimal weight: 1.9990 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** B 499 ASN A 370 ASN A 499 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.141755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.123093 restraints weight = 14638.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.125973 restraints weight = 9078.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.127938 restraints weight = 6541.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.129215 restraints weight = 5188.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.130237 restraints weight = 4415.800| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2393 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= 0.135 Angle : 0.555 6.611 13786 Z= 0.286 Chirality : 0.042 0.253 1542 Planarity : 0.004 0.050 1714 Dihedral : 9.755 153.251 1440 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.29 % Favored : 95.54 % Rotamer: Outliers : 2.70 % Allowed : 15.03 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.25), residues: 1188 helix: 1.42 (0.19), residues: 816 sheet: -0.66 (0.95), residues: 28 loop : -1.50 (0.35), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 268 TYR 0.013 0.001 TYR B 589 PHE 0.016 0.001 PHE A 61 TRP 0.032 0.001 TRP A 155 HIS 0.003 0.001 HIS B 130 Details of bonding type rmsd covalent geometry : bond 0.00307 (10156) covalent geometry : angle 0.55452 (13786) hydrogen bonds : bond 0.03863 ( 598) hydrogen bonds : angle 3.84507 ( 1752) *********************** 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 117 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 89 time to evaluate : 0.348 Fit side-chains REVERT: B 504 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7605 (pm20) REVERT: A 117 VAL cc_start: 0.8587 (t) cc_final: 0.8327 (p) REVERT: A 305 GLU cc_start: 0.8152 (tp30) cc_final: 0.7920 (tp30) REVERT: A 504 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7708 (pm20) outliers start: 28 outliers final: 21 residues processed: 114 average time/residue: 0.0952 time to fit residues: 15.2114 Evaluate side-chains 109 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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 499 ASN 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 209 SER 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 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 499 ASN 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 98 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 112 optimal weight: 0.4980 chunk 64 optimal weight: 0.9980 chunk 90 optimal weight: 0.0870 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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 499 ASN A 370 ASN ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.142425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.123751 restraints weight = 14548.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.126630 restraints weight = 9046.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.128626 restraints weight = 6533.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.130002 restraints weight = 5165.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.130916 restraints weight = 4367.876| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.2439 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= 0.124 Angle : 0.554 7.277 13786 Z= 0.283 Chirality : 0.042 0.250 1542 Planarity : 0.004 0.045 1714 Dihedral : 9.726 164.157 1440 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.55 % Favored : 95.37 % Rotamer: Outliers : 2.41 % Allowed : 15.51 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.25), residues: 1188 helix: 1.48 (0.19), residues: 816 sheet: -0.65 (0.95), residues: 28 loop : -1.47 (0.35), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 268 TYR 0.014 0.001 TYR B 589 PHE 0.022 0.001 PHE B 22 TRP 0.034 0.002 TRP A 155 HIS 0.003 0.001 HIS B 130 Details of bonding type rmsd covalent geometry : bond 0.00276 (10156) covalent geometry : angle 0.55362 (13786) hydrogen bonds : bond 0.03826 ( 598) hydrogen bonds : angle 3.82394 ( 1752) ********************** 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: 25 poor density : 88 time to evaluate : 0.367 Fit side-chains REVERT: B 224 ILE cc_start: 0.8696 (mm) cc_final: 0.8341 (mt) REVERT: B 305 GLU cc_start: 0.8114 (tp30) cc_final: 0.7815 (tp30) REVERT: A 117 VAL cc_start: 0.8474 (t) cc_final: 0.8226 (p) REVERT: A 305 GLU cc_start: 0.8175 (tp30) cc_final: 0.7957 (tp30) REVERT: A 504 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7687 (pm20) outliers start: 25 outliers final: 20 residues processed: 108 average time/residue: 0.1026 time to fit residues: 15.5169 Evaluate side-chains 109 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 0.362 ------------------------------------------------------------------------------- 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 499 ASN Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 590 MET Chi-restraints excluded: chain B residue 595 HIS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 5 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 117 optimal weight: 0.5980 chunk 74 optimal weight: 0.5980 chunk 90 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 116 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 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** B 499 ASN A 370 ASN A 499 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.141312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.122480 restraints weight = 14736.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.125356 restraints weight = 9193.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.127253 restraints weight = 6645.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.128652 restraints weight = 5298.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.129503 restraints weight = 4488.926| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2443 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= 0.149 Angle : 0.566 6.617 13786 Z= 0.292 Chirality : 0.043 0.250 1542 Planarity : 0.004 0.037 1714 Dihedral : 9.787 172.213 1440 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.41 % Allowed : 15.32 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.25), residues: 1188 helix: 1.45 (0.19), residues: 814 sheet: -0.70 (0.95), residues: 28 loop : -1.48 (0.35), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 498 TYR 0.014 0.001 TYR A 654 PHE 0.017 0.001 PHE A 197 TRP 0.036 0.002 TRP A 155 HIS 0.003 0.001 HIS B 619 Details of bonding type rmsd covalent geometry : bond 0.00344 (10156) covalent geometry : angle 0.56619 (13786) hydrogen bonds : bond 0.03951 ( 598) hydrogen bonds : angle 3.86868 ( 1752) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1368.15 seconds wall clock time: 24 minutes 23.24 seconds (1463.24 seconds total)