Starting phenix.real_space_refine on Sun Dec 29 05:09:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7psl_13613/12_2024/7psl_13613.cif Found real_map, /net/cci-nas-00/data/ceres_data/7psl_13613/12_2024/7psl_13613.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7psl_13613/12_2024/7psl_13613.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7psl_13613/12_2024/7psl_13613.map" model { file = "/net/cci-nas-00/data/ceres_data/7psl_13613/12_2024/7psl_13613.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7psl_13613/12_2024/7psl_13613.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.070 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 34 5.16 5 C 6190 2.51 5 N 1634 2.21 5 O 1750 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 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: 9612 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4756 Classifications: {'peptide': 600} Link IDs: {'PTRANS': 17, 'TRANS': 582} Chain: "A" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 50 Unusual residues: {'LOP': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B Time building chain proxies: 9.64, per 1000 atoms: 1.00 Number of scatterers: 9612 At special positions: 0 Unit cell: (109.647, 76.167, 142.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 34 16.00 P 4 15.00 O 1750 8.00 N 1634 7.00 C 6190 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: 3.19 Conformation dependent library (CDL) restraints added in 1.2 seconds 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2244 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 6 sheets defined 68.4% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 92 through 99 Processing helix chain 'A' and resid 104 through 140 removed outlier: 3.916A pdb=" N ARG A 108 " --> pdb=" O ASN A 104 " (cutoff:3.500A) Proline residue: A 129 - end of helix Processing helix chain 'A' and resid 151 through 199 removed outlier: 4.073A pdb=" N THR A 157 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASN A 185 " --> pdb=" O LYS A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 209 removed outlier: 3.630A pdb=" N ARG A 209 " --> pdb=" O TRP A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 234 Processing helix chain 'A' and resid 236 through 254 removed outlier: 3.626A pdb=" N PHE A 254 " --> pdb=" O LEU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 304 removed outlier: 4.178A pdb=" N ALA A 259 " --> pdb=" O GLY A 255 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA A 294 " --> pdb=" O ALA A 290 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN A 304 " --> pdb=" O ASP A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 311 removed outlier: 3.726A pdb=" N PHE A 311 " --> pdb=" O ALA A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 365 Processing helix chain 'A' and resid 366 through 368 No H-bonds generated for 'chain 'A' and resid 366 through 368' Processing helix chain 'A' and resid 371 through 387 removed outlier: 3.527A pdb=" N LEU A 375 " --> pdb=" O THR A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 412 removed outlier: 3.942A pdb=" N LEU A 392 " --> pdb=" O PRO A 388 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ARG A 397 " --> pdb=" O GLY A 393 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ASP A 398 " --> pdb=" O SER A 394 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LYS A 400 " --> pdb=" O TYR A 396 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N GLN A 401 " --> pdb=" O ARG A 397 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A 412 " --> pdb=" O THR A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 483 Processing helix chain 'A' and resid 504 through 510 Processing helix chain 'A' and resid 526 through 532 Processing helix chain 'A' and resid 538 through 549 Processing helix chain 'A' and resid 551 through 556 Processing helix chain 'A' and resid 574 through 590 Processing helix chain 'A' and resid 604 through 619 Processing helix chain 'A' and resid 632 through 636 Processing helix chain 'A' and resid 655 through 661 Processing helix chain 'A' and resid 665 through 691 removed outlier: 3.800A pdb=" N GLU A 669 " --> pdb=" O SER A 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 99 Processing helix chain 'B' and resid 104 through 140 removed outlier: 3.916A pdb=" N ARG B 108 " --> pdb=" O ASN B 104 " (cutoff:3.500A) Proline residue: B 129 - end of helix Processing helix chain 'B' and resid 151 through 199 removed outlier: 4.074A pdb=" N THR B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASN B 185 " --> pdb=" O LYS B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 209 removed outlier: 3.629A pdb=" N ARG B 209 " --> pdb=" O TRP B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 234 Processing helix chain 'B' and resid 236 through 254 removed outlier: 3.626A pdb=" N PHE B 254 " --> pdb=" O LEU B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 304 removed outlier: 4.179A pdb=" N ALA B 259 " --> pdb=" O GLY B 255 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA B 294 " --> pdb=" O ALA B 290 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN B 304 " --> pdb=" O ASP B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 311 removed outlier: 3.726A pdb=" N PHE B 311 " --> pdb=" O ALA B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 365 Processing helix chain 'B' and resid 366 through 368 No H-bonds generated for 'chain 'B' and resid 366 through 368' Processing helix chain 'B' and resid 371 through 387 removed outlier: 3.527A pdb=" N LEU B 375 " --> pdb=" O THR B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 412 removed outlier: 3.942A pdb=" N LEU B 392 " --> pdb=" O PRO B 388 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ARG B 397 " --> pdb=" O GLY B 393 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ASP B 398 " --> pdb=" O SER B 394 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LYS B 400 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N GLN B 401 " --> pdb=" O ARG B 397 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU B 412 " --> pdb=" O THR B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 483 Processing helix chain 'B' and resid 504 through 510 Processing helix chain 'B' and resid 526 through 532 Processing helix chain 'B' and resid 538 through 549 Processing helix chain 'B' and resid 551 through 556 Processing helix chain 'B' and resid 574 through 590 Processing helix chain 'B' and resid 604 through 619 Processing helix chain 'B' and resid 632 through 636 Processing helix chain 'B' and resid 655 through 661 Processing helix chain 'B' and resid 665 through 691 removed outlier: 3.800A pdb=" N GLU B 669 " --> pdb=" O SER B 665 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 438 through 439 Processing sheet with id=AA2, first strand: chain 'A' and resid 441 through 443 removed outlier: 7.148A pdb=" N PHE A 443 " --> pdb=" O LYS A 453 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N LYS A 453 " --> pdb=" O PHE A 443 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 512 through 515 removed outlier: 7.026A pdb=" N THR A 465 " --> pdb=" O TYR A 628 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ALA A 466 " --> pdb=" O ILE A 643 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LEU A 645 " --> pdb=" O ALA A 466 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL A 468 " --> pdb=" O LEU A 645 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 438 through 439 Processing sheet with id=AA5, first strand: chain 'B' and resid 441 through 443 removed outlier: 7.148A pdb=" N PHE B 443 " --> pdb=" O LYS B 453 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N LYS B 453 " --> pdb=" O PHE B 443 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 512 through 515 removed outlier: 7.026A pdb=" N THR B 465 " --> pdb=" O TYR B 628 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ALA B 466 " --> pdb=" O ILE B 643 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LEU B 645 " --> pdb=" O ALA B 466 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL B 468 " --> pdb=" O LEU B 645 " (cutoff:3.500A) 637 hydrogen bonds defined for protein. 1881 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: 2.98 Time building geometry restraints manager: 3.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1552 1.31 - 1.43: 2487 1.43 - 1.56: 5683 1.56 - 1.68: 4 1.68 - 1.81: 62 Bond restraints: 9788 Sorted by residual: bond pdb=" C24 LOP B 701 " pdb=" O6 LOP B 701 " ideal model delta sigma weight residual 1.325 1.397 -0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" C24 LOP A 701 " pdb=" O6 LOP A 701 " ideal model delta sigma weight residual 1.325 1.397 -0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" C6 LOP A 701 " pdb=" O5 LOP A 701 " ideal model delta sigma weight residual 1.331 1.400 -0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C6 LOP B 701 " pdb=" O5 LOP B 701 " ideal model delta sigma weight residual 1.331 1.400 -0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" O3 PO4 A 702 " pdb=" P PO4 A 702 " ideal model delta sigma weight residual 1.569 1.519 0.050 2.00e-02 2.50e+03 6.23e+00 ... (remaining 9783 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 13055 2.26 - 4.52: 145 4.52 - 6.79: 16 6.79 - 9.05: 6 9.05 - 11.31: 4 Bond angle restraints: 13226 Sorted by residual: angle pdb=" N ILE B 526 " pdb=" CA ILE B 526 " pdb=" C ILE B 526 " ideal model delta sigma weight residual 113.42 108.14 5.28 1.17e+00 7.31e-01 2.04e+01 angle pdb=" N ILE A 526 " pdb=" CA ILE A 526 " pdb=" C ILE A 526 " ideal model delta sigma weight residual 113.42 108.14 5.28 1.17e+00 7.31e-01 2.04e+01 angle pdb=" N ILE B 154 " pdb=" CA ILE B 154 " pdb=" C ILE B 154 " ideal model delta sigma weight residual 112.96 109.16 3.80 1.00e+00 1.00e+00 1.44e+01 angle pdb=" N ILE A 154 " pdb=" CA ILE A 154 " pdb=" C ILE A 154 " ideal model delta sigma weight residual 112.96 109.16 3.80 1.00e+00 1.00e+00 1.44e+01 angle pdb=" O3 LOP A 701 " pdb=" P1 LOP A 701 " pdb=" O4 LOP A 701 " ideal model delta sigma weight residual 120.67 109.36 11.31 3.00e+00 1.11e-01 1.42e+01 ... (remaining 13221 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 5158 17.54 - 35.07: 574 35.07 - 52.61: 134 52.61 - 70.14: 24 70.14 - 87.68: 4 Dihedral angle restraints: 5894 sinusoidal: 2420 harmonic: 3474 Sorted by residual: dihedral pdb=" CA ASP A 374 " pdb=" CB ASP A 374 " pdb=" CG ASP A 374 " pdb=" OD1 ASP A 374 " ideal model delta sinusoidal sigma weight residual -30.00 -89.21 59.21 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CA ASP B 374 " pdb=" CB ASP B 374 " pdb=" CG ASP B 374 " pdb=" OD1 ASP B 374 " ideal model delta sinusoidal sigma weight residual -30.00 -89.18 59.18 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CA ARG B 484 " pdb=" C ARG B 484 " pdb=" N PHE B 485 " pdb=" CA PHE B 485 " ideal model delta harmonic sigma weight residual 180.00 164.32 15.68 0 5.00e+00 4.00e-02 9.83e+00 ... (remaining 5891 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1096 0.039 - 0.078: 329 0.078 - 0.116: 83 0.116 - 0.155: 14 0.155 - 0.194: 2 Chirality restraints: 1524 Sorted by residual: chirality pdb=" C4 LOP B 701 " pdb=" C3 LOP B 701 " pdb=" C5 LOP B 701 " pdb=" O5 LOP B 701 " both_signs ideal model delta sigma weight residual False -2.34 -2.53 0.19 2.00e-01 2.50e+01 9.39e-01 chirality pdb=" C4 LOP A 701 " pdb=" C3 LOP A 701 " pdb=" C5 LOP A 701 " pdb=" O5 LOP A 701 " both_signs ideal model delta sigma weight residual False -2.34 -2.53 0.19 2.00e-01 2.50e+01 9.17e-01 chirality pdb=" CA PRO A 129 " pdb=" N PRO A 129 " pdb=" C PRO A 129 " pdb=" CB PRO A 129 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.13 2.00e-01 2.50e+01 4.54e-01 ... (remaining 1521 not shown) Planarity restraints: 1664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 128 " -0.023 5.00e-02 4.00e+02 3.44e-02 1.89e+00 pdb=" N PRO A 129 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 129 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 129 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 128 " 0.023 5.00e-02 4.00e+02 3.40e-02 1.85e+00 pdb=" N PRO B 129 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 129 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 129 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 387 " -0.019 5.00e-02 4.00e+02 2.87e-02 1.32e+00 pdb=" N PRO A 388 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 388 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 388 " -0.016 5.00e-02 4.00e+02 ... (remaining 1661 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2326 2.79 - 3.32: 9919 3.32 - 3.84: 15409 3.84 - 4.37: 17523 4.37 - 4.90: 31515 Nonbonded interactions: 76692 Sorted by model distance: nonbonded pdb=" OD1 ASP A 499 " pdb=" N ILE A 500 " model vdw 2.258 3.120 nonbonded pdb=" OD1 ASP B 499 " pdb=" N ILE B 500 " model vdw 2.259 3.120 nonbonded pdb=" NZ LYS A 531 " pdb=" O ILE A 535 " model vdw 2.297 3.120 nonbonded pdb=" NZ LYS B 531 " pdb=" O ILE B 535 " model vdw 2.297 3.120 nonbonded pdb=" O THR A 273 " pdb=" OG1 THR A 277 " model vdw 2.311 3.040 ... (remaining 76687 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=0.00 max=1.00 mean=0.94 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.880 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: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 30.640 Find NCS groups from input model: 0.330 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: 0.010 Load rotamer database and sin/cos tables:3.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 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 : 0.006 0.072 9788 Z= 0.418 Angle : 0.649 11.311 13226 Z= 0.342 Chirality : 0.040 0.194 1524 Planarity : 0.003 0.034 1664 Dihedral : 15.096 87.681 3650 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % 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: -3.04 (0.22), residues: 1196 helix: -0.93 (0.17), residues: 778 sheet: -3.80 (0.67), residues: 56 loop : -4.02 (0.27), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 279 HIS 0.002 0.001 HIS B 656 PHE 0.012 0.001 PHE A 132 TYR 0.008 0.001 TYR B 310 ARG 0.002 0.000 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 ARG cc_start: 0.8202 (ttp80) cc_final: 0.7884 (ttp80) REVERT: A 649 ARG cc_start: 0.7714 (mtt180) cc_final: 0.7013 (mtp-110) REVERT: A 665 SER cc_start: 0.8387 (m) cc_final: 0.8121 (p) REVERT: A 668 ARG cc_start: 0.8517 (mtp180) cc_final: 0.8178 (mtm180) REVERT: B 312 ASN cc_start: 0.8628 (m110) cc_final: 0.8422 (m110) REVERT: B 668 ARG cc_start: 0.8484 (mtp180) cc_final: 0.8130 (mtm180) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.2704 time to fit residues: 47.1386 Evaluate side-chains 100 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN A 196 GLN A 346 GLN A 606 HIS B 127 GLN B 196 GLN B 346 GLN ** B 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 606 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 9788 Z= 0.250 Angle : 0.561 7.533 13226 Z= 0.291 Chirality : 0.041 0.227 1524 Planarity : 0.004 0.035 1664 Dihedral : 8.194 56.750 1378 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.78 % Allowed : 10.56 % Favored : 88.66 % 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: -0.63 (0.24), residues: 1196 helix: 1.00 (0.18), residues: 780 sheet: -3.81 (0.66), residues: 56 loop : -3.08 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 279 HIS 0.005 0.001 HIS B 197 PHE 0.020 0.002 PHE A 132 TYR 0.032 0.002 TYR A 310 ARG 0.003 0.000 ARG B 632 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 126 time to evaluate : 0.913 Fit side-chains revert: symmetry clash REVERT: A 97 ARG cc_start: 0.8108 (ttp80) cc_final: 0.7835 (tmm160) REVERT: A 594 MET cc_start: 0.7368 (mmt) cc_final: 0.7026 (mmt) REVERT: A 662 MET cc_start: 0.6974 (mtp) cc_final: 0.6740 (ptp) REVERT: A 668 ARG cc_start: 0.8600 (mtp180) cc_final: 0.8256 (mtm180) REVERT: B 148 VAL cc_start: 0.8816 (p) cc_final: 0.8605 (m) REVERT: B 668 ARG cc_start: 0.8526 (mtp180) cc_final: 0.8166 (mtm180) outliers start: 8 outliers final: 6 residues processed: 131 average time/residue: 0.2591 time to fit residues: 46.4064 Evaluate side-chains 114 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 108 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 390 ASN Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 390 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 117 optimal weight: 10.0000 chunk 97 optimal weight: 6.9990 chunk 108 optimal weight: 0.7980 chunk 37 optimal weight: 6.9990 chunk 87 optimal weight: 6.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 HIS B 235 HIS ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 9788 Z= 0.441 Angle : 0.655 8.915 13226 Z= 0.341 Chirality : 0.045 0.243 1524 Planarity : 0.004 0.030 1664 Dihedral : 8.390 58.657 1378 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.13 % Allowed : 13.95 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.54 (0.25), residues: 1196 helix: 0.96 (0.18), residues: 798 sheet: -3.64 (0.67), residues: 56 loop : -2.97 (0.31), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 279 HIS 0.005 0.001 HIS A 606 PHE 0.022 0.002 PHE A 132 TYR 0.040 0.002 TYR B 310 ARG 0.005 0.000 ARG A 632 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 1.646 Fit side-chains revert: symmetry clash REVERT: A 97 ARG cc_start: 0.8152 (ttp80) cc_final: 0.7882 (ttp80) REVERT: A 252 TYR cc_start: 0.8668 (t80) cc_final: 0.8435 (t80) REVERT: A 594 MET cc_start: 0.7524 (mmt) cc_final: 0.7118 (mmt) REVERT: A 662 MET cc_start: 0.6997 (mtp) cc_final: 0.6749 (mtt) REVERT: A 668 ARG cc_start: 0.8625 (mtp180) cc_final: 0.8224 (mtm180) REVERT: B 148 VAL cc_start: 0.8872 (p) cc_final: 0.8631 (m) REVERT: B 216 ARG cc_start: 0.6956 (ttp80) cc_final: 0.6635 (ttp80) REVERT: B 594 MET cc_start: 0.7491 (mmt) cc_final: 0.7135 (mmt) REVERT: B 662 MET cc_start: 0.6564 (mtp) cc_final: 0.6276 (ptp) REVERT: B 668 ARG cc_start: 0.8567 (mtp180) cc_final: 0.8180 (mtm180) outliers start: 22 outliers final: 15 residues processed: 165 average time/residue: 0.2298 time to fit residues: 52.9670 Evaluate side-chains 150 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 135 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 390 ASN Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 659 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 56 optimal weight: 0.1980 chunk 12 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 109 optimal weight: 0.5980 chunk 115 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9788 Z= 0.185 Angle : 0.529 9.208 13226 Z= 0.273 Chirality : 0.039 0.240 1524 Planarity : 0.003 0.029 1664 Dihedral : 8.045 59.818 1378 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.13 % Allowed : 15.50 % Favored : 82.36 % 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 (0.26), residues: 1196 helix: 1.59 (0.19), residues: 798 sheet: -3.52 (0.55), residues: 80 loop : -2.50 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 279 HIS 0.004 0.001 HIS A 606 PHE 0.016 0.001 PHE B 179 TYR 0.038 0.002 TYR B 310 ARG 0.006 0.000 ARG A 632 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 1.121 Fit side-chains revert: symmetry clash REVERT: A 97 ARG cc_start: 0.8047 (ttp80) cc_final: 0.7786 (ttp80) REVERT: A 594 MET cc_start: 0.7357 (mmt) cc_final: 0.7117 (mmt) REVERT: A 649 ARG cc_start: 0.7412 (ttm170) cc_final: 0.6680 (mtp-110) REVERT: A 662 MET cc_start: 0.7025 (mtp) cc_final: 0.6721 (ptp) REVERT: A 668 ARG cc_start: 0.8608 (mtp180) cc_final: 0.8228 (mtm180) REVERT: B 148 VAL cc_start: 0.8820 (p) cc_final: 0.8556 (m) REVERT: B 216 ARG cc_start: 0.6958 (ttp80) cc_final: 0.6638 (ttp80) REVERT: B 668 ARG cc_start: 0.8583 (mtp180) cc_final: 0.8350 (mtp180) outliers start: 22 outliers final: 15 residues processed: 160 average time/residue: 0.2310 time to fit residues: 51.4914 Evaluate side-chains 155 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 140 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 390 ASN Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 659 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 1 optimal weight: 0.0870 chunk 86 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 80 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 104 optimal weight: 1.9990 chunk 29 optimal weight: 0.4980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9788 Z= 0.175 Angle : 0.513 9.261 13226 Z= 0.263 Chirality : 0.039 0.254 1524 Planarity : 0.003 0.031 1664 Dihedral : 7.656 57.587 1378 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.13 % Allowed : 17.83 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.26), residues: 1196 helix: 1.95 (0.19), residues: 796 sheet: -3.45 (0.56), residues: 80 loop : -2.11 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 279 HIS 0.003 0.001 HIS A 606 PHE 0.021 0.001 PHE B 254 TYR 0.029 0.002 TYR A 310 ARG 0.007 0.000 ARG A 632 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 ARG cc_start: 0.7956 (ttp80) cc_final: 0.7708 (ttp80) REVERT: A 156 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7634 (tp) REVERT: A 594 MET cc_start: 0.7300 (mmt) cc_final: 0.7096 (mmt) REVERT: A 649 ARG cc_start: 0.7356 (ttm170) cc_final: 0.6627 (mtp-110) REVERT: A 662 MET cc_start: 0.7039 (mtp) cc_final: 0.6800 (mtp) REVERT: A 668 ARG cc_start: 0.8592 (mtp180) cc_final: 0.8225 (mtm180) REVERT: B 97 ARG cc_start: 0.8134 (tmm160) cc_final: 0.7793 (ttp80) REVERT: B 148 VAL cc_start: 0.8778 (p) cc_final: 0.8504 (m) REVERT: B 216 ARG cc_start: 0.6952 (ttp80) cc_final: 0.6626 (ttp80) REVERT: B 668 ARG cc_start: 0.8552 (mtp180) cc_final: 0.8257 (mtp180) outliers start: 22 outliers final: 11 residues processed: 157 average time/residue: 0.2297 time to fit residues: 50.1827 Evaluate side-chains 149 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 137 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 659 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 116 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 9788 Z= 0.262 Angle : 0.553 9.726 13226 Z= 0.282 Chirality : 0.040 0.248 1524 Planarity : 0.003 0.026 1664 Dihedral : 7.579 56.966 1378 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.03 % Allowed : 18.31 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.76 (0.26), residues: 1196 helix: 1.86 (0.19), residues: 796 sheet: -3.38 (0.57), residues: 80 loop : -1.99 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 279 HIS 0.003 0.001 HIS B 606 PHE 0.026 0.002 PHE A 254 TYR 0.023 0.002 TYR A 310 ARG 0.002 0.000 ARG A 484 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 ARG cc_start: 0.7965 (ttp80) cc_final: 0.7734 (ttp80) REVERT: A 594 MET cc_start: 0.7369 (mmt) cc_final: 0.7016 (mmt) REVERT: A 662 MET cc_start: 0.6993 (mtp) cc_final: 0.6741 (mtp) REVERT: A 668 ARG cc_start: 0.8586 (mtp180) cc_final: 0.8202 (mtm180) REVERT: B 97 ARG cc_start: 0.8153 (tmm160) cc_final: 0.7814 (ttp80) REVERT: B 148 VAL cc_start: 0.8822 (p) cc_final: 0.8552 (m) REVERT: B 216 ARG cc_start: 0.6985 (ttp80) cc_final: 0.6653 (ttp80) REVERT: B 668 ARG cc_start: 0.8567 (mtp180) cc_final: 0.8273 (mtp180) outliers start: 21 outliers final: 16 residues processed: 159 average time/residue: 0.2273 time to fit residues: 50.7480 Evaluate side-chains 153 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 536 ASP Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 659 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 84 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 chunk 115 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 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 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9788 Z= 0.215 Angle : 0.541 11.637 13226 Z= 0.273 Chirality : 0.039 0.234 1524 Planarity : 0.003 0.022 1664 Dihedral : 7.416 56.710 1378 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.84 % Allowed : 19.86 % Favored : 78.29 % 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 (0.26), residues: 1196 helix: 2.03 (0.19), residues: 792 sheet: -3.35 (0.57), residues: 80 loop : -1.58 (0.38), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 279 HIS 0.002 0.001 HIS B 656 PHE 0.021 0.001 PHE A 254 TYR 0.022 0.002 TYR A 310 ARG 0.002 0.000 ARG B 165 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 ARG cc_start: 0.7948 (ttp80) cc_final: 0.7720 (ttp80) REVERT: A 594 MET cc_start: 0.7362 (mmt) cc_final: 0.7030 (mmt) REVERT: A 662 MET cc_start: 0.7016 (mtp) cc_final: 0.6759 (mtp) REVERT: A 668 ARG cc_start: 0.8590 (mtp180) cc_final: 0.8203 (mtm180) REVERT: B 97 ARG cc_start: 0.8132 (tmm160) cc_final: 0.7786 (ttp80) REVERT: B 148 VAL cc_start: 0.8819 (p) cc_final: 0.8537 (m) REVERT: B 216 ARG cc_start: 0.6990 (ttp80) cc_final: 0.6622 (ttp80) REVERT: B 662 MET cc_start: 0.6113 (ptp) cc_final: 0.5896 (pmm) outliers start: 19 outliers final: 16 residues processed: 149 average time/residue: 0.2329 time to fit residues: 48.3372 Evaluate side-chains 148 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 659 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 0.0870 chunk 46 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 overall best weight: 1.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9788 Z= 0.270 Angle : 0.563 9.393 13226 Z= 0.288 Chirality : 0.040 0.216 1524 Planarity : 0.003 0.023 1664 Dihedral : 7.367 56.250 1378 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.52 % Allowed : 19.67 % Favored : 77.81 % 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: 0.89 (0.26), residues: 1196 helix: 1.90 (0.19), residues: 796 sheet: -3.31 (0.58), residues: 80 loop : -1.74 (0.37), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 279 HIS 0.002 0.001 HIS A 656 PHE 0.019 0.002 PHE A 254 TYR 0.022 0.002 TYR A 310 ARG 0.006 0.000 ARG B 668 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 140 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 ARG cc_start: 0.7943 (ttp80) cc_final: 0.7715 (ttp80) REVERT: A 594 MET cc_start: 0.7366 (mmt) cc_final: 0.7001 (mmt) REVERT: A 668 ARG cc_start: 0.8597 (mtp180) cc_final: 0.8281 (mtp180) REVERT: B 97 ARG cc_start: 0.8142 (tmm160) cc_final: 0.7804 (ttp80) REVERT: B 148 VAL cc_start: 0.8858 (p) cc_final: 0.8592 (m) REVERT: B 216 ARG cc_start: 0.6985 (ttp80) cc_final: 0.6610 (ttp80) outliers start: 26 outliers final: 21 residues processed: 156 average time/residue: 0.2341 time to fit residues: 50.8701 Evaluate side-chains 155 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 536 ASP Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 659 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 3.9990 chunk 101 optimal weight: 0.5980 chunk 107 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9788 Z= 0.207 Angle : 0.545 9.087 13226 Z= 0.277 Chirality : 0.039 0.209 1524 Planarity : 0.003 0.043 1664 Dihedral : 7.278 58.943 1378 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.03 % Allowed : 20.35 % Favored : 77.62 % 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: 1.21 (0.26), residues: 1196 helix: 2.10 (0.19), residues: 792 sheet: -3.29 (0.57), residues: 80 loop : -1.43 (0.37), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 279 HIS 0.002 0.001 HIS B 656 PHE 0.016 0.001 PHE A 254 TYR 0.029 0.002 TYR A 310 ARG 0.011 0.000 ARG B 668 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 ARG cc_start: 0.7890 (ttp80) cc_final: 0.7666 (ttp80) REVERT: A 594 MET cc_start: 0.7355 (mmt) cc_final: 0.7014 (mmt) REVERT: A 668 ARG cc_start: 0.8579 (mtp180) cc_final: 0.8267 (mtp180) REVERT: B 97 ARG cc_start: 0.8123 (tmm160) cc_final: 0.7780 (ttp80) REVERT: B 148 VAL cc_start: 0.8842 (p) cc_final: 0.8567 (m) REVERT: B 216 ARG cc_start: 0.6976 (ttp80) cc_final: 0.6597 (ttp80) outliers start: 21 outliers final: 20 residues processed: 145 average time/residue: 0.2305 time to fit residues: 46.5055 Evaluate side-chains 148 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 659 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 119 optimal weight: 7.9990 chunk 110 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 58 optimal weight: 5.9990 chunk 75 optimal weight: 0.5980 chunk 101 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9788 Z= 0.217 Angle : 0.563 9.342 13226 Z= 0.284 Chirality : 0.039 0.213 1524 Planarity : 0.003 0.027 1664 Dihedral : 7.238 59.893 1378 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.13 % Allowed : 20.35 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.26), residues: 1196 helix: 2.16 (0.19), residues: 790 sheet: -3.28 (0.57), residues: 80 loop : -1.41 (0.37), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 279 HIS 0.003 0.001 HIS B 656 PHE 0.017 0.001 PHE B 254 TYR 0.024 0.001 TYR A 310 ARG 0.005 0.000 ARG B 632 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 132 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 ARG cc_start: 0.7882 (ttp80) cc_final: 0.7658 (ttp80) REVERT: A 594 MET cc_start: 0.7352 (mmt) cc_final: 0.7012 (mmt) REVERT: B 97 ARG cc_start: 0.8101 (tmm160) cc_final: 0.7752 (ttp80) REVERT: B 148 VAL cc_start: 0.8851 (p) cc_final: 0.8582 (m) REVERT: B 216 ARG cc_start: 0.6986 (ttp80) cc_final: 0.6606 (ttp80) outliers start: 22 outliers final: 20 residues processed: 147 average time/residue: 0.2388 time to fit residues: 48.8312 Evaluate side-chains 151 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 536 ASP Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 611 LEU 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: 0.6980 chunk 26 optimal weight: 0.7980 chunk 95 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 97 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.176549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.126830 restraints weight = 10490.099| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.57 r_work: 0.3319 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9788 Z= 0.221 Angle : 0.565 9.799 13226 Z= 0.284 Chirality : 0.039 0.206 1524 Planarity : 0.003 0.025 1664 Dihedral : 7.191 59.042 1378 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.03 % Allowed : 20.25 % Favored : 77.71 % 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: 1.29 (0.26), residues: 1196 helix: 2.18 (0.18), residues: 790 sheet: -3.30 (0.57), residues: 80 loop : -1.40 (0.37), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 279 HIS 0.003 0.001 HIS B 656 PHE 0.015 0.001 PHE B 254 TYR 0.024 0.002 TYR A 310 ARG 0.006 0.000 ARG B 668 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2109.49 seconds wall clock time: 39 minutes 24.59 seconds (2364.59 seconds total)