Starting phenix.real_space_refine on Wed Mar 4 01:31:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7psl_13613/03_2026/7psl_13613.cif Found real_map, /net/cci-nas-00/data/ceres_data/7psl_13613/03_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_13613/03_2026/7psl_13613.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7psl_13613/03_2026/7psl_13613.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7psl_13613/03_2026/7psl_13613.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7psl_13613/03_2026/7psl_13613.map" } 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-5986/lib/python3.9/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: 3.59, per 1000 atoms: 0.37 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: 1.01 Conformation dependent library (CDL) restraints added in 579.7 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: 0.29 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: 1.26 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: 0.02 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: 2.920 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.850 Find NCS groups from input model: 0.070 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.220 ------------------------------------------------------------------------------- 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= 0.266 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 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 covalent geometry : bond 0.00638 ( 9788) covalent geometry : angle 0.64925 (13226) hydrogen bonds : bond 0.10273 ( 637) hydrogen bonds : angle 5.28085 ( 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 : 0.249 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: 0.1143 time to fit residues: 20.0203 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 : 0.314 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 127 GLN A 606 HIS B 127 GLN B 196 GLN ** B 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 606 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.182320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.136320 restraints weight = 10109.155| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 2.53 r_work: 0.3441 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 9788 Z= 0.156 Angle : 0.543 8.146 13226 Z= 0.282 Chirality : 0.040 0.241 1524 Planarity : 0.003 0.034 1664 Dihedral : 8.096 56.301 1378 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.78 % Allowed : 10.08 % Favored : 89.15 % 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: -0.53 (0.25), residues: 1196 helix: 1.10 (0.18), residues: 780 sheet: -3.82 (0.65), residues: 56 loop : -3.11 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 632 TYR 0.030 0.002 TYR A 310 PHE 0.017 0.002 PHE A 532 TRP 0.013 0.001 TRP B 279 HIS 0.004 0.001 HIS B 197 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 9788) covalent geometry : angle 0.54335 (13226) hydrogen bonds : bond 0.05209 ( 637) hydrogen bonds : angle 4.02335 ( 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 130 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 122 time to evaluate : 0.233 Fit side-chains revert: symmetry clash REVERT: A 97 ARG cc_start: 0.8143 (ttp80) cc_final: 0.7831 (tmm160) REVERT: A 594 MET cc_start: 0.7629 (mmt) cc_final: 0.7359 (mmt) REVERT: A 662 MET cc_start: 0.6842 (mtp) cc_final: 0.6628 (ptp) REVERT: A 668 ARG cc_start: 0.8642 (mtp180) cc_final: 0.8202 (mtm180) REVERT: B 148 VAL cc_start: 0.8633 (p) cc_final: 0.8430 (m) REVERT: B 668 ARG cc_start: 0.8589 (mtp180) cc_final: 0.8117 (mtm180) outliers start: 8 outliers final: 6 residues processed: 127 average time/residue: 0.1025 time to fit residues: 17.7366 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 : 0.336 ------------------------------------------------------------------------------- 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: 0.8980 chunk 92 optimal weight: 2.9990 chunk 95 optimal weight: 0.0570 chunk 111 optimal weight: 0.0020 chunk 64 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 21 optimal weight: 0.0570 chunk 40 optimal weight: 2.9990 overall best weight: 0.3024 ------------------------------------------------------------------------------- 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 = 0.4086 r_free = 0.4086 target = 0.184430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.138364 restraints weight = 10117.772| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.55 r_work: 0.3463 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9788 Z= 0.120 Angle : 0.505 7.860 13226 Z= 0.260 Chirality : 0.038 0.229 1524 Planarity : 0.003 0.026 1664 Dihedral : 7.647 55.405 1378 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.26 % Allowed : 11.72 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.44 (0.26), residues: 1196 helix: 1.79 (0.19), residues: 798 sheet: -3.82 (0.52), residues: 80 loop : -2.58 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 632 TYR 0.035 0.001 TYR B 310 PHE 0.018 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 covalent geometry : bond 0.00252 ( 9788) covalent geometry : angle 0.50495 (13226) hydrogen bonds : bond 0.04738 ( 637) hydrogen bonds : angle 3.70483 ( 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 131 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 0.324 Fit side-chains revert: symmetry clash REVERT: A 216 ARG cc_start: 0.6910 (ttp80) cc_final: 0.6559 (ttp80) REVERT: A 668 ARG cc_start: 0.8668 (mtp180) cc_final: 0.8276 (mtm180) REVERT: B 97 ARG cc_start: 0.8110 (tmm160) cc_final: 0.7793 (ttp80) REVERT: B 148 VAL cc_start: 0.8669 (p) cc_final: 0.8408 (m) REVERT: B 594 MET cc_start: 0.7418 (mmt) cc_final: 0.7080 (mmt) REVERT: B 662 MET cc_start: 0.6652 (mtp) cc_final: 0.6307 (ptp) REVERT: B 668 ARG cc_start: 0.8637 (mtp180) cc_final: 0.8208 (mtm180) outliers start: 13 outliers final: 8 residues processed: 125 average time/residue: 0.0971 time to fit residues: 17.1098 Evaluate side-chains 116 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 108 time to evaluate : 0.381 ------------------------------------------------------------------------------- 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 573 ILE Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 524 ASP 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: 2.9990 chunk 20 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 38 optimal weight: 7.9990 chunk 30 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 5 optimal weight: 0.4980 chunk 92 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN A 346 GLN B 312 ASN B 346 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.175563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.126674 restraints weight = 10581.225| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.57 r_work: 0.3337 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9788 Z= 0.168 Angle : 0.549 9.332 13226 Z= 0.282 Chirality : 0.041 0.255 1524 Planarity : 0.003 0.032 1664 Dihedral : 7.479 56.912 1378 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.45 % Allowed : 13.86 % Favored : 84.69 % 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: 0.51 (0.26), residues: 1196 helix: 1.77 (0.19), residues: 794 sheet: -3.64 (0.55), residues: 80 loop : -2.30 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 632 TYR 0.035 0.002 TYR B 310 PHE 0.017 0.002 PHE A 132 TRP 0.007 0.001 TRP B 279 HIS 0.003 0.001 HIS A 606 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 9788) covalent geometry : angle 0.54877 (13226) hydrogen bonds : bond 0.05187 ( 637) hydrogen bonds : angle 3.75013 ( 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 163 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 148 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 ARG cc_start: 0.8076 (tmm160) cc_final: 0.7867 (ttp80) REVERT: A 216 ARG cc_start: 0.7031 (ttp80) cc_final: 0.6614 (ttp80) REVERT: A 668 ARG cc_start: 0.8693 (mtp180) cc_final: 0.8333 (mtm180) REVERT: B 97 ARG cc_start: 0.8177 (tmm160) cc_final: 0.7878 (ttp80) REVERT: B 148 VAL cc_start: 0.8688 (p) cc_final: 0.8423 (m) REVERT: B 216 ARG cc_start: 0.7004 (ttp80) cc_final: 0.6533 (ttp80) REVERT: B 662 MET cc_start: 0.6780 (mtp) cc_final: 0.6450 (ptp) REVERT: B 668 ARG cc_start: 0.8672 (mtp180) cc_final: 0.8210 (mtm180) outliers start: 15 outliers final: 8 residues processed: 158 average time/residue: 0.0954 time to fit residues: 21.0336 Evaluate side-chains 138 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 130 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 41 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 101 optimal weight: 0.8980 chunk 68 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 116 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 98 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.178825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.129890 restraints weight = 10516.193| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.60 r_work: 0.3344 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9788 Z= 0.139 Angle : 0.522 10.431 13226 Z= 0.265 Chirality : 0.039 0.244 1524 Planarity : 0.003 0.022 1664 Dihedral : 7.365 57.117 1378 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.55 % Allowed : 16.09 % 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 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: 0.80 (0.26), residues: 1196 helix: 1.97 (0.19), residues: 794 sheet: -3.60 (0.55), residues: 80 loop : -2.08 (0.36), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 632 TYR 0.031 0.002 TYR A 310 PHE 0.019 0.002 PHE A 254 TRP 0.009 0.001 TRP A 279 HIS 0.003 0.001 HIS B 606 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 9788) covalent geometry : angle 0.52153 (13226) hydrogen bonds : bond 0.04926 ( 637) hydrogen bonds : angle 3.64553 ( 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 155 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 139 time to evaluate : 0.272 Fit side-chains revert: symmetry clash REVERT: A 97 ARG cc_start: 0.8027 (tmm160) cc_final: 0.7819 (ttp80) REVERT: A 216 ARG cc_start: 0.7042 (ttp80) cc_final: 0.6581 (ttp80) REVERT: A 662 MET cc_start: 0.6022 (ptp) cc_final: 0.5765 (ptp) REVERT: A 668 ARG cc_start: 0.8663 (mtp180) cc_final: 0.8180 (mtp180) REVERT: B 97 ARG cc_start: 0.8142 (tmm160) cc_final: 0.7839 (ttp80) REVERT: B 148 VAL cc_start: 0.8659 (p) cc_final: 0.8389 (m) REVERT: B 216 ARG cc_start: 0.7009 (ttp80) cc_final: 0.6536 (ttp80) REVERT: B 662 MET cc_start: 0.6818 (mtp) cc_final: 0.6456 (ptp) REVERT: B 668 ARG cc_start: 0.8638 (mtp180) cc_final: 0.8153 (mtm180) outliers start: 16 outliers final: 9 residues processed: 150 average time/residue: 0.0915 time to fit residues: 19.3458 Evaluate side-chains 143 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 134 time to evaluate : 0.336 ------------------------------------------------------------------------------- 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 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 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: 0.9980 chunk 80 optimal weight: 4.9990 chunk 29 optimal weight: 0.4980 chunk 25 optimal weight: 0.5980 chunk 58 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 32 optimal weight: 0.0970 chunk 26 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.180323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.132214 restraints weight = 10435.354| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.50 r_work: 0.3381 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.2812 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= 0.123 Angle : 0.505 9.331 13226 Z= 0.257 Chirality : 0.038 0.237 1524 Planarity : 0.003 0.024 1664 Dihedral : 7.167 57.279 1378 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.45 % Allowed : 17.25 % Favored : 81.30 % 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: 1.17 (0.26), residues: 1196 helix: 2.18 (0.19), residues: 790 sheet: -3.58 (0.55), residues: 80 loop : -1.64 (0.37), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 509 TYR 0.025 0.001 TYR A 310 PHE 0.028 0.001 PHE A 254 TRP 0.009 0.001 TRP A 279 HIS 0.002 0.001 HIS B 606 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 9788) covalent geometry : angle 0.50519 (13226) hydrogen bonds : bond 0.04692 ( 637) hydrogen bonds : angle 3.54091 ( 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 156 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 141 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: A 97 ARG cc_start: 0.7895 (tmm160) cc_final: 0.7691 (ttp80) REVERT: A 216 ARG cc_start: 0.6856 (ttp80) cc_final: 0.6360 (ttp80) REVERT: A 662 MET cc_start: 0.6129 (ptp) cc_final: 0.5873 (ptp) REVERT: A 668 ARG cc_start: 0.8665 (mtp180) cc_final: 0.8185 (mtp180) REVERT: B 97 ARG cc_start: 0.8052 (tmm160) cc_final: 0.7741 (ttp80) REVERT: B 148 VAL cc_start: 0.8573 (p) cc_final: 0.8307 (m) REVERT: B 216 ARG cc_start: 0.6823 (ttp80) cc_final: 0.6339 (ttp80) REVERT: B 594 MET cc_start: 0.7256 (mmt) cc_final: 0.6996 (mmt) REVERT: B 662 MET cc_start: 0.6793 (mtp) cc_final: 0.6431 (ptp) REVERT: B 668 ARG cc_start: 0.8645 (mtp180) cc_final: 0.8167 (mtm180) outliers start: 15 outliers final: 11 residues processed: 152 average time/residue: 0.0996 time to fit residues: 21.0405 Evaluate side-chains 144 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 133 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 SER 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 156 LEU Chi-restraints excluded: chain B residue 312 ASN Chi-restraints excluded: chain B residue 386 SER 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 86 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 115 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.178785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.130294 restraints weight = 10450.449| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.50 r_work: 0.3364 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9788 Z= 0.138 Angle : 0.513 9.210 13226 Z= 0.262 Chirality : 0.039 0.231 1524 Planarity : 0.003 0.021 1664 Dihedral : 7.049 57.081 1378 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.55 % Allowed : 18.22 % Favored : 80.23 % 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: 1.26 (0.26), residues: 1196 helix: 2.22 (0.19), residues: 790 sheet: -3.49 (0.55), residues: 80 loop : -1.55 (0.37), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 616 TYR 0.018 0.002 TYR B 310 PHE 0.025 0.001 PHE B 254 TRP 0.008 0.001 TRP A 279 HIS 0.002 0.001 HIS A 656 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 9788) covalent geometry : angle 0.51292 (13226) hydrogen bonds : bond 0.04782 ( 637) hydrogen bonds : angle 3.53199 ( 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: 16 poor density : 136 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 ARG cc_start: 0.7874 (tmm160) cc_final: 0.7669 (ttp80) REVERT: A 216 ARG cc_start: 0.6858 (ttp80) cc_final: 0.6367 (ttp80) REVERT: A 668 ARG cc_start: 0.8641 (mtp180) cc_final: 0.8261 (mtm180) REVERT: B 97 ARG cc_start: 0.8001 (tmm160) cc_final: 0.7683 (ttp80) REVERT: B 148 VAL cc_start: 0.8574 (p) cc_final: 0.8301 (m) REVERT: B 216 ARG cc_start: 0.6830 (ttp80) cc_final: 0.6329 (ttp80) REVERT: B 594 MET cc_start: 0.7216 (mmt) cc_final: 0.6950 (mmt) REVERT: B 662 MET cc_start: 0.6807 (mtp) cc_final: 0.6431 (ptp) REVERT: B 668 ARG cc_start: 0.8655 (mtp180) cc_final: 0.8182 (mtm180) outliers start: 16 outliers final: 11 residues processed: 146 average time/residue: 0.1091 time to fit residues: 21.9340 Evaluate side-chains 145 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 134 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 SER 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 156 LEU Chi-restraints excluded: chain B residue 312 ASN Chi-restraints excluded: chain B residue 386 SER 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: 0.4980 chunk 46 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 65 optimal weight: 0.0670 chunk 34 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 312 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.179903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.131571 restraints weight = 10521.684| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.51 r_work: 0.3377 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.3013 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= 0.122 Angle : 0.510 9.208 13226 Z= 0.259 Chirality : 0.038 0.221 1524 Planarity : 0.003 0.025 1664 Dihedral : 6.989 56.771 1378 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.45 % Allowed : 18.70 % Favored : 79.84 % 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: 1.44 (0.26), residues: 1196 helix: 2.36 (0.19), residues: 790 sheet: -3.42 (0.55), residues: 80 loop : -1.49 (0.37), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 632 TYR 0.017 0.001 TYR B 310 PHE 0.022 0.001 PHE B 254 TRP 0.008 0.001 TRP B 279 HIS 0.002 0.001 HIS B 606 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 9788) covalent geometry : angle 0.50975 (13226) hydrogen bonds : bond 0.04627 ( 637) hydrogen bonds : angle 3.47762 ( 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 152 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 ARG cc_start: 0.7836 (tmm160) cc_final: 0.7630 (ttp80) REVERT: A 216 ARG cc_start: 0.6861 (ttp80) cc_final: 0.6361 (ttp80) REVERT: A 668 ARG cc_start: 0.8650 (mtp180) cc_final: 0.8195 (mtp180) REVERT: B 97 ARG cc_start: 0.7933 (tmm160) cc_final: 0.7618 (ttp80) REVERT: B 148 VAL cc_start: 0.8601 (p) cc_final: 0.8331 (m) REVERT: B 216 ARG cc_start: 0.6824 (ttp80) cc_final: 0.6333 (ttp80) REVERT: B 662 MET cc_start: 0.6818 (mtp) cc_final: 0.6428 (ptp) REVERT: B 668 ARG cc_start: 0.8647 (mtp180) cc_final: 0.8166 (mtm180) outliers start: 15 outliers final: 13 residues processed: 145 average time/residue: 0.0948 time to fit residues: 18.8839 Evaluate side-chains 146 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 time to evaluate : 0.292 ------------------------------------------------------------------------------- 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 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 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: 0.9980 chunk 105 optimal weight: 6.9990 chunk 49 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 45 optimal weight: 0.1980 chunk 97 optimal weight: 6.9990 chunk 115 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.176961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.127872 restraints weight = 10526.148| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.58 r_work: 0.3349 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.3087 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= 0.142 Angle : 0.532 11.483 13226 Z= 0.269 Chirality : 0.039 0.217 1524 Planarity : 0.003 0.027 1664 Dihedral : 7.018 57.206 1378 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.65 % Allowed : 18.90 % 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: 2.33 (0.18), residues: 790 sheet: -3.43 (0.55), residues: 80 loop : -1.43 (0.38), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 632 TYR 0.022 0.002 TYR A 310 PHE 0.021 0.001 PHE A 443 TRP 0.006 0.001 TRP B 279 HIS 0.002 0.001 HIS B 606 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 9788) covalent geometry : angle 0.53181 (13226) hydrogen bonds : bond 0.04770 ( 637) hydrogen bonds : angle 3.50378 ( 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 153 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 ARG cc_start: 0.7926 (tmm160) cc_final: 0.7712 (ttp80) REVERT: A 216 ARG cc_start: 0.7054 (ttp80) cc_final: 0.6573 (ttp80) REVERT: A 668 ARG cc_start: 0.8648 (mtp180) cc_final: 0.8220 (mtp180) REVERT: B 97 ARG cc_start: 0.7989 (tmm160) cc_final: 0.7667 (ttp80) REVERT: B 148 VAL cc_start: 0.8657 (p) cc_final: 0.8384 (m) REVERT: B 216 ARG cc_start: 0.7058 (ttp80) cc_final: 0.6568 (ttp80) REVERT: B 662 MET cc_start: 0.6836 (mtp) cc_final: 0.6448 (ptp) REVERT: B 668 ARG cc_start: 0.8642 (mtp180) cc_final: 0.8189 (mtm180) outliers start: 17 outliers final: 15 residues processed: 145 average time/residue: 0.0987 time to fit residues: 19.9878 Evaluate side-chains 147 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 0.376 ------------------------------------------------------------------------------- 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 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 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: 1.9990 chunk 51 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 109 optimal weight: 0.6980 chunk 119 optimal weight: 9.9990 chunk 114 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 6.9990 chunk 94 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 312 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.175977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.126865 restraints weight = 10541.598| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.55 r_work: 0.3342 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9788 Z= 0.153 Angle : 0.541 10.961 13226 Z= 0.275 Chirality : 0.039 0.207 1524 Planarity : 0.003 0.026 1664 Dihedral : 7.059 57.536 1378 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.55 % Allowed : 18.90 % Favored : 79.55 % 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: 1.44 (0.26), residues: 1196 helix: 2.34 (0.18), residues: 788 sheet: -3.47 (0.55), residues: 80 loop : -1.40 (0.37), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 632 TYR 0.020 0.002 TYR A 310 PHE 0.020 0.002 PHE A 443 TRP 0.006 0.001 TRP B 100 HIS 0.002 0.001 HIS B 606 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 9788) covalent geometry : angle 0.54080 (13226) hydrogen bonds : bond 0.04870 ( 637) hydrogen bonds : angle 3.52918 ( 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 152 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 136 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 ARG cc_start: 0.7934 (tmm160) cc_final: 0.7718 (ttp80) REVERT: A 216 ARG cc_start: 0.7085 (ttp80) cc_final: 0.6594 (ttp80) REVERT: A 668 ARG cc_start: 0.8637 (mtp180) cc_final: 0.8225 (mtp180) REVERT: B 97 ARG cc_start: 0.7997 (tmm160) cc_final: 0.7676 (ttp80) REVERT: B 148 VAL cc_start: 0.8679 (p) cc_final: 0.8408 (m) REVERT: B 216 ARG cc_start: 0.7077 (ttp80) cc_final: 0.6572 (ttp80) REVERT: B 662 MET cc_start: 0.6835 (mtp) cc_final: 0.6435 (ptp) REVERT: B 668 ARG cc_start: 0.8641 (mtp180) cc_final: 0.8186 (mtm180) outliers start: 16 outliers final: 15 residues processed: 143 average time/residue: 0.0936 time to fit residues: 18.7338 Evaluate side-chains 146 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 0.330 ------------------------------------------------------------------------------- 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 156 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 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 63 optimal weight: 0.5980 chunk 86 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 47 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 110 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 312 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.178696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.129740 restraints weight = 10524.590| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.57 r_work: 0.3354 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.3221 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= 0.136 Angle : 0.534 9.963 13226 Z= 0.273 Chirality : 0.038 0.208 1524 Planarity : 0.003 0.024 1664 Dihedral : 7.049 58.115 1378 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.74 % Allowed : 18.99 % Favored : 79.26 % 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: 1.50 (0.26), residues: 1196 helix: 2.39 (0.18), residues: 790 sheet: -3.45 (0.55), residues: 80 loop : -1.37 (0.38), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 632 TYR 0.019 0.001 TYR A 310 PHE 0.019 0.001 PHE A 443 TRP 0.007 0.001 TRP A 279 HIS 0.002 0.001 HIS A 656 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 9788) covalent geometry : angle 0.53442 (13226) hydrogen bonds : bond 0.04764 ( 637) hydrogen bonds : angle 3.49966 ( 1881) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1954.22 seconds wall clock time: 34 minutes 10.05 seconds (2050.05 seconds total)