Starting phenix.real_space_refine on Thu Jul 2 19:13:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7psl_13613/07_2026/7psl_13613.cif Found real_map, /net/cci-nas-00/data/ceres_data/7psl_13613/07_2026/7psl_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 { model { file = "/net/cci-nas-00/data/ceres_data/7psl_13613/07_2026/7psl_13613.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7psl_13613/07_2026/7psl_13613.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7psl_13613/07_2026/7psl_13613.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7psl_13613/07_2026/7psl_13613.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7psl_13613/07_2026/7psl_13613.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7psl_13613/07_2026/7psl_13613.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.070 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: 4.17, per 1000 atoms: 0.43 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: 1.24 Conformation dependent library (CDL) restraints added in 363.0 milliseconds 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: 0.27 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: 1.55 Time building geometry restraints manager: 1.53 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: 5152 17.54 - 35.07: 570 35.07 - 52.61: 126 52.61 - 70.14: 22 70.14 - 87.68: 4 Dihedral angle restraints: 5874 sinusoidal: 2400 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 5871 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 3.110 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: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 12.520 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 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= 0.266 Angle : 0.649 11.311 13226 Z= 0.342 Chirality : 0.040 0.194 1524 Planarity : 0.003 0.034 1664 Dihedral : 14.908 87.681 3630 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 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: -3.04 (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 ARG 0.002 0.000 ARG A 280 TYR 0.008 0.001 TYR B 310 PHE 0.012 0.001 PHE A 132 TRP 0.013 0.001 TRP B 279 HIS 0.002 0.001 HIS B 656 Details of bonding type rmsd/Z covalent geometry : bond 0.00638 / 0.27 ( 9788) covalent geometry : angle 0.64925 / 0.34 (13226) hydrogen bonds : bond 0.10273 / 6.56 ( 637) hydrogen bonds : angle 5.28085 / 3.83 ( 1881) *********************** 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 : 0.352 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: 0.1175 time to fit residues: 20.7344 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 : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.2980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 9.9990 chunk 117 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 127 GLN A 606 HIS B 127 GLN ** B 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 606 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.184009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.137925 restraints weight = 10127.286| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.50 r_work: 0.3448 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 9788 Z= 0.146 Angle : 0.551 7.910 13226 Z= 0.285 Chirality : 0.040 0.239 1524 Planarity : 0.004 0.034 1664 Dihedral : 7.710 59.260 1358 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.87 % Allowed : 9.59 % Favored : 89.53 % 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: -0.34 (0.25), residues: 1196 helix: 1.23 (0.19), residues: 780 sheet: -3.82 (0.64), residues: 56 loop : -2.99 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 632 TYR 0.033 0.002 TYR A 310 PHE 0.017 0.002 PHE A 132 TRP 0.013 0.001 TRP B 279 HIS 0.004 0.001 HIS B 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 ( 9788) covalent geometry : angle 0.55085 / 0.28 (13226) hydrogen bonds : bond 0.05166 / 3.45 ( 637) hydrogen bonds : angle 3.98600 / 2.91 ( 1881) *********************** 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: 9 poor density : 125 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: A 97 ARG cc_start: 0.8079 (ttp80) cc_final: 0.7764 (tmm160) REVERT: A 216 ARG cc_start: 0.6758 (ttp80) cc_final: 0.6458 (ttp80) REVERT: A 594 MET cc_start: 0.7484 (mmt) cc_final: 0.7020 (mmt) REVERT: A 662 MET cc_start: 0.6838 (mtp) cc_final: 0.6598 (ptp) REVERT: A 668 ARG cc_start: 0.8652 (mtp180) cc_final: 0.8186 (mtm180) REVERT: B 148 VAL cc_start: 0.8590 (p) cc_final: 0.8383 (m) REVERT: B 668 ARG cc_start: 0.8601 (mtp180) cc_final: 0.8111 (mtm180) outliers start: 9 outliers final: 6 residues processed: 130 average time/residue: 0.1134 time to fit residues: 20.2134 Evaluate side-chains 116 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 110 time to evaluate : 0.351 ------------------------------------------------------------------------------- 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 28 optimal weight: 0.5980 chunk 92 optimal weight: 0.0470 chunk 95 optimal weight: 5.9990 chunk 111 optimal weight: 0.0970 chunk 64 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 346 GLN ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.183337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.136949 restraints weight = 10165.175| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.54 r_work: 0.3446 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9788 Z= 0.118 Angle : 0.509 9.212 13226 Z= 0.260 Chirality : 0.039 0.245 1524 Planarity : 0.003 0.028 1664 Dihedral : 7.235 59.582 1358 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.45 % Allowed : 11.92 % Favored : 86.63 % 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: 0.50 (0.26), residues: 1196 helix: 1.82 (0.19), residues: 798 sheet: -3.75 (0.53), residues: 80 loop : -2.51 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 632 TYR 0.039 0.002 TYR B 310 PHE 0.019 0.001 PHE A 532 TRP 0.011 0.001 TRP B 279 HIS 0.005 0.001 HIS A 606 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 ( 9788) covalent geometry : angle 0.50944 / 0.26 (13226) hydrogen bonds : bond 0.04737 / 3.15 ( 637) hydrogen bonds : angle 3.66313 / 2.66 ( 1881) *********************** 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 135 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 216 ARG cc_start: 0.6922 (ttp80) cc_final: 0.6544 (ttp80) REVERT: A 668 ARG cc_start: 0.8679 (mtp180) cc_final: 0.8280 (mtm180) REVERT: B 97 ARG cc_start: 0.8118 (tmm160) cc_final: 0.7804 (ttp80) REVERT: B 216 ARG cc_start: 0.6899 (ttp80) cc_final: 0.6414 (ttp80) REVERT: B 662 MET cc_start: 0.5994 (mtt) cc_final: 0.5732 (ptp) REVERT: B 668 ARG cc_start: 0.8633 (mtp180) cc_final: 0.8199 (mtm180) outliers start: 15 outliers final: 9 residues processed: 128 average time/residue: 0.1023 time to fit residues: 18.4959 Evaluate side-chains 116 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 107 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 573 ILE Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 390 ASN 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 15 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 5 optimal weight: 0.0870 chunk 92 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 GLN B 196 GLN B 312 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.179316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.131453 restraints weight = 10470.081| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.59 r_work: 0.3388 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2387 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= 0.137 Angle : 0.508 9.110 13226 Z= 0.260 Chirality : 0.039 0.254 1524 Planarity : 0.003 0.029 1664 Dihedral : 6.940 59.418 1358 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.36 % Allowed : 13.76 % Favored : 84.88 % 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: 0.78 (0.26), residues: 1196 helix: 1.97 (0.19), residues: 796 sheet: -3.58 (0.54), residues: 80 loop : -2.21 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 632 TYR 0.031 0.002 TYR B 310 PHE 0.016 0.001 PHE A 179 TRP 0.007 0.001 TRP A 279 HIS 0.003 0.001 HIS A 606 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 9788) covalent geometry : angle 0.50809 / 0.26 (13226) hydrogen bonds : bond 0.04806 / 3.21 ( 637) hydrogen bonds : angle 3.61850 / 2.62 ( 1881) *********************** 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 158 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 144 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: A 216 ARG cc_start: 0.6978 (ttp80) cc_final: 0.6553 (ttp80) REVERT: A 668 ARG cc_start: 0.8683 (mtp180) cc_final: 0.8312 (mtm180) REVERT: B 97 ARG cc_start: 0.8137 (tmm160) cc_final: 0.7826 (ttp80) REVERT: B 216 ARG cc_start: 0.6953 (ttp80) cc_final: 0.6478 (ttp80) REVERT: B 668 ARG cc_start: 0.8647 (mtp180) cc_final: 0.8340 (mtp180) outliers start: 14 outliers final: 7 residues processed: 153 average time/residue: 0.0953 time to fit residues: 20.5692 Evaluate side-chains 128 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 121 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 SER 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 573 ILE 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 37 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 88 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 116 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 105 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 312 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.173963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.125024 restraints weight = 10640.165| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.48 r_work: 0.3300 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.2687 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= 0.237 Angle : 0.602 10.782 13226 Z= 0.307 Chirality : 0.043 0.247 1524 Planarity : 0.003 0.023 1664 Dihedral : 7.187 58.894 1358 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.84 % Allowed : 16.28 % Favored : 81.88 % 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: 0.45 (0.26), residues: 1196 helix: 1.65 (0.19), residues: 794 sheet: -3.67 (0.65), residues: 56 loop : -2.27 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 585 TYR 0.031 0.002 TYR A 310 PHE 0.022 0.002 PHE A 254 TRP 0.008 0.001 TRP B 100 HIS 0.003 0.001 HIS B 606 Details of bonding type rmsd/Z covalent geometry : bond 0.00582 / 0.24 ( 9788) covalent geometry : angle 0.60187 / 0.31 (13226) hydrogen bonds : bond 0.05586 / 3.75 ( 637) hydrogen bonds : angle 3.87244 / 2.80 ( 1881) *********************** 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 164 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 145 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 216 ARG cc_start: 0.6911 (ttp80) cc_final: 0.6455 (ttp80) REVERT: A 668 ARG cc_start: 0.8693 (mtp180) cc_final: 0.8476 (ttm170) REVERT: B 97 ARG cc_start: 0.8158 (tmm160) cc_final: 0.7855 (ttp80) REVERT: B 216 ARG cc_start: 0.6912 (ttp80) cc_final: 0.6441 (ttp80) REVERT: B 668 ARG cc_start: 0.8663 (mtp180) cc_final: 0.8270 (mtp180) outliers start: 19 outliers final: 13 residues processed: 158 average time/residue: 0.0974 time to fit residues: 21.7831 Evaluate side-chains 148 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 135 time to evaluate : 0.362 ------------------------------------------------------------------------------- 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 404 ILE Chi-restraints excluded: chain A residue 437 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 265 THR Chi-restraints excluded: chain B residue 312 ASN Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 464 LYS Chi-restraints excluded: chain B residue 573 ILE 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 83 optimal weight: 0.5980 chunk 80 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 58 optimal weight: 9.9990 chunk 22 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 32 optimal weight: 0.0370 chunk 26 optimal weight: 0.5980 chunk 62 optimal weight: 0.6980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.178997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.130498 restraints weight = 10482.602| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.51 r_work: 0.3361 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.2846 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= 0.127 Angle : 0.531 11.711 13226 Z= 0.266 Chirality : 0.038 0.233 1524 Planarity : 0.003 0.025 1664 Dihedral : 6.930 59.914 1358 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.65 % Allowed : 17.93 % Favored : 80.43 % 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: 1.06 (0.26), residues: 1196 helix: 2.07 (0.19), residues: 788 sheet: -3.59 (0.55), residues: 80 loop : -1.61 (0.37), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 632 TYR 0.034 0.002 TYR B 310 PHE 0.029 0.001 PHE A 254 TRP 0.010 0.001 TRP A 279 HIS 0.002 0.001 HIS B 606 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 ( 9788) covalent geometry : angle 0.53056 / 0.27 (13226) hydrogen bonds : bond 0.04848 / 3.24 ( 637) hydrogen bonds : angle 3.60298 / 2.60 ( 1881) *********************** 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 153 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 216 ARG cc_start: 0.6903 (ttp80) cc_final: 0.6419 (ttp80) REVERT: A 662 MET cc_start: 0.6266 (ptp) cc_final: 0.6048 (ptp) REVERT: A 668 ARG cc_start: 0.8673 (mtp180) cc_final: 0.8196 (mtp180) REVERT: B 97 ARG cc_start: 0.8097 (tmm160) cc_final: 0.7783 (ttp80) REVERT: B 216 ARG cc_start: 0.6870 (ttp80) cc_final: 0.6378 (ttp80) REVERT: B 594 MET cc_start: 0.7360 (mmt) cc_final: 0.6969 (mmt) REVERT: B 662 MET cc_start: 0.5853 (ptp) cc_final: 0.5639 (pmm) REVERT: B 668 ARG cc_start: 0.8674 (mtp180) cc_final: 0.8266 (mtp180) outliers start: 17 outliers final: 12 residues processed: 148 average time/residue: 0.0961 time to fit residues: 19.9947 Evaluate side-chains 143 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 131 time to evaluate : 0.390 ------------------------------------------------------------------------------- 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 437 THR Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 312 ASN Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 464 LYS Chi-restraints excluded: chain B residue 573 ILE 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 86 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 chunk 73 optimal weight: 0.5980 chunk 62 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 115 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 312 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.177143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.128038 restraints weight = 10522.210| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.59 r_work: 0.3348 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.2961 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= 0.131 Angle : 0.524 9.746 13226 Z= 0.263 Chirality : 0.038 0.232 1524 Planarity : 0.003 0.023 1664 Dihedral : 6.756 59.843 1358 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.65 % Allowed : 18.70 % 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 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: 1.21 (0.26), residues: 1196 helix: 2.18 (0.19), residues: 790 sheet: -3.54 (0.55), residues: 80 loop : -1.55 (0.37), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 632 TYR 0.021 0.002 TYR A 310 PHE 0.033 0.001 PHE A 254 TRP 0.009 0.001 TRP A 279 HIS 0.002 0.001 HIS A 656 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 9788) covalent geometry : angle 0.52386 / 0.26 (13226) hydrogen bonds : bond 0.04813 / 3.22 ( 637) hydrogen bonds : angle 3.55534 / 2.57 ( 1881) *********************** 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 152 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 216 ARG cc_start: 0.7053 (ttp80) cc_final: 0.6566 (ttp80) REVERT: A 662 MET cc_start: 0.6371 (ptp) cc_final: 0.6154 (ptp) REVERT: A 668 ARG cc_start: 0.8649 (mtp180) cc_final: 0.8202 (mtp180) REVERT: B 97 ARG cc_start: 0.8066 (tmm160) cc_final: 0.7748 (ttp80) REVERT: B 216 ARG cc_start: 0.7016 (ttp80) cc_final: 0.6514 (ttp80) REVERT: B 594 MET cc_start: 0.7384 (mmt) cc_final: 0.7058 (mmt) REVERT: B 662 MET cc_start: 0.6117 (ptp) cc_final: 0.5903 (ptt) REVERT: B 668 ARG cc_start: 0.8675 (mtp180) cc_final: 0.8286 (mtp180) outliers start: 17 outliers final: 14 residues processed: 146 average time/residue: 0.0896 time to fit residues: 18.5111 Evaluate side-chains 145 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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 437 THR Chi-restraints excluded: chain A residue 464 LYS 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 312 ASN Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 464 LYS 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 106 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 11 optimal weight: 0.0770 chunk 65 optimal weight: 0.0370 chunk 34 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.4416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.180517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.132153 restraints weight = 10516.859| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.51 r_work: 0.3385 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9788 Z= 0.119 Angle : 0.519 8.873 13226 Z= 0.263 Chirality : 0.038 0.220 1524 Planarity : 0.003 0.022 1664 Dihedral : 6.587 59.711 1358 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.23 % Allowed : 18.31 % Favored : 79.46 % 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: 1.43 (0.26), residues: 1196 helix: 2.37 (0.19), residues: 788 sheet: -3.44 (0.55), residues: 80 loop : -1.49 (0.37), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 632 TYR 0.020 0.001 TYR B 310 PHE 0.021 0.001 PHE B 254 TRP 0.009 0.001 TRP B 279 HIS 0.002 0.001 HIS B 656 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 ( 9788) covalent geometry : angle 0.51914 / 0.26 (13226) hydrogen bonds : bond 0.04606 / 3.07 ( 637) hydrogen bonds : angle 3.48380 / 2.52 ( 1881) *********************** 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 158 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 216 ARG cc_start: 0.6872 (ttp80) cc_final: 0.6364 (ttp80) REVERT: A 668 ARG cc_start: 0.8664 (mtp180) cc_final: 0.8463 (ttm170) REVERT: B 97 ARG cc_start: 0.7929 (tmm160) cc_final: 0.7611 (ttp80) REVERT: B 216 ARG cc_start: 0.6835 (ttp80) cc_final: 0.6339 (ttp80) REVERT: B 668 ARG cc_start: 0.8638 (mtp180) cc_final: 0.8337 (mtp180) outliers start: 23 outliers final: 18 residues processed: 152 average time/residue: 0.0859 time to fit residues: 18.5810 Evaluate side-chains 148 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 464 LYS 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 312 ASN Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 464 LYS Chi-restraints excluded: chain B residue 477 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 83 optimal weight: 0.9990 chunk 105 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 71 optimal weight: 0.0370 chunk 45 optimal weight: 0.3980 chunk 97 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 overall best weight: 0.6462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 312 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.177867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.129022 restraints weight = 10508.409| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.58 r_work: 0.3349 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9788 Z= 0.130 Angle : 0.537 11.714 13226 Z= 0.266 Chirality : 0.038 0.207 1524 Planarity : 0.003 0.020 1664 Dihedral : 6.479 59.293 1358 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.65 % Allowed : 19.48 % Favored : 78.88 % 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: 1.51 (0.26), residues: 1196 helix: 2.42 (0.19), residues: 788 sheet: -3.39 (0.56), residues: 80 loop : -1.43 (0.37), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 632 TYR 0.017 0.001 TYR A 310 PHE 0.016 0.001 PHE B 254 TRP 0.007 0.001 TRP B 279 HIS 0.002 0.001 HIS A 656 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 9788) covalent geometry : angle 0.53684 / 0.27 (13226) hydrogen bonds : bond 0.04668 / 3.12 ( 637) hydrogen bonds : angle 3.49183 / 2.52 ( 1881) *********************** 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 150 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 0.297 Fit side-chains revert: symmetry clash REVERT: A 216 ARG cc_start: 0.7052 (ttp80) cc_final: 0.6577 (ttp80) REVERT: B 97 ARG cc_start: 0.7985 (tmm160) cc_final: 0.7661 (ttp80) REVERT: B 216 ARG cc_start: 0.7032 (ttp80) cc_final: 0.6543 (ttp80) REVERT: B 594 MET cc_start: 0.7437 (mmt) cc_final: 0.7018 (mmt) REVERT: B 668 ARG cc_start: 0.8630 (mtp180) cc_final: 0.8343 (mtp180) outliers start: 17 outliers final: 16 residues processed: 144 average time/residue: 0.0792 time to fit residues: 16.2738 Evaluate side-chains 142 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 437 THR 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 312 ASN Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 464 LYS Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 514 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 80 optimal weight: 4.9990 chunk 39 optimal weight: 0.0270 chunk 51 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 109 optimal weight: 0.6980 chunk 119 optimal weight: 6.9990 chunk 114 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 312 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.179898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.130887 restraints weight = 10474.873| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.59 r_work: 0.3364 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9788 Z= 0.133 Angle : 0.550 12.974 13226 Z= 0.272 Chirality : 0.039 0.218 1524 Planarity : 0.003 0.047 1664 Dihedral : 6.483 59.774 1358 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.13 % Allowed : 19.09 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.26), residues: 1196 helix: 2.45 (0.18), residues: 790 sheet: -3.38 (0.55), residues: 80 loop : -1.39 (0.37), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 668 TYR 0.018 0.001 TYR A 310 PHE 0.017 0.001 PHE B 254 TRP 0.007 0.001 TRP A 279 HIS 0.002 0.001 HIS A 656 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 9788) covalent geometry : angle 0.54967 / 0.27 (13226) hydrogen bonds : bond 0.04676 / 3.12 ( 637) hydrogen bonds : angle 3.49130 / 2.52 ( 1881) ********************** 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 151 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 216 ARG cc_start: 0.7045 (ttp80) cc_final: 0.6560 (ttp80) REVERT: A 668 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.7590 (mtt180) REVERT: B 97 ARG cc_start: 0.7968 (tmm160) cc_final: 0.7647 (ttp80) REVERT: B 216 ARG cc_start: 0.7053 (ttp80) cc_final: 0.6535 (ttp80) REVERT: B 668 ARG cc_start: 0.8633 (mtp180) cc_final: 0.8361 (mtp180) outliers start: 22 outliers final: 17 residues processed: 141 average time/residue: 0.0812 time to fit residues: 16.1712 Evaluate side-chains 146 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 437 THR 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 668 ARG Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 312 ASN Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain B residue 464 LYS Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 519 THR 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 63 optimal weight: 0.5980 chunk 86 optimal weight: 0.5980 chunk 79 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 chunk 114 optimal weight: 5.9990 chunk 110 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.177162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.128059 restraints weight = 10561.707| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.58 r_work: 0.3351 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.3323 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= 0.143 Angle : 0.573 13.239 13226 Z= 0.279 Chirality : 0.039 0.221 1524 Planarity : 0.003 0.036 1664 Dihedral : 6.521 59.522 1358 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.13 % Allowed : 19.19 % Favored : 78.68 % 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: 1.54 (0.26), residues: 1196 helix: 2.42 (0.18), residues: 790 sheet: -3.42 (0.55), residues: 80 loop : -1.38 (0.37), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 668 TYR 0.018 0.002 TYR A 310 PHE 0.016 0.001 PHE B 254 TRP 0.006 0.001 TRP A 279 HIS 0.002 0.001 HIS A 656 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 ( 9788) covalent geometry : angle 0.57348 / 0.28 (13226) hydrogen bonds : bond 0.04767 / 3.19 ( 637) hydrogen bonds : angle 3.52401 / 2.54 ( 1881) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1966.60 seconds wall clock time: 34 minutes 25.75 seconds (2065.75 seconds total)