Starting phenix.real_space_refine on Fri Feb 14 06:15:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7psl_13613/02_2025/7psl_13613.cif Found real_map, /net/cci-nas-00/data/ceres_data/7psl_13613/02_2025/7psl_13613.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7psl_13613/02_2025/7psl_13613.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7psl_13613/02_2025/7psl_13613.map" model { file = "/net/cci-nas-00/data/ceres_data/7psl_13613/02_2025/7psl_13613.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7psl_13613/02_2025/7psl_13613.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.070 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 34 5.16 5 C 6190 2.51 5 N 1634 2.21 5 O 1750 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9612 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4756 Classifications: {'peptide': 600} Link IDs: {'PTRANS': 17, 'TRANS': 582} Chain: "A" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 50 Unusual residues: {'LOP': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B Time building chain proxies: 8.87, per 1000 atoms: 0.92 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: 2.59 Conformation dependent library (CDL) restraints added in 1.1 seconds 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2244 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 6 sheets defined 68.4% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 92 through 99 Processing helix chain 'A' and resid 104 through 140 removed outlier: 3.916A pdb=" N ARG A 108 " --> pdb=" O ASN A 104 " (cutoff:3.500A) Proline residue: A 129 - end of helix Processing helix chain 'A' and resid 151 through 199 removed outlier: 4.073A pdb=" N THR A 157 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASN A 185 " --> pdb=" O LYS A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 209 removed outlier: 3.630A pdb=" N ARG A 209 " --> pdb=" O TRP A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 234 Processing helix chain 'A' and resid 236 through 254 removed outlier: 3.626A pdb=" N PHE A 254 " --> pdb=" O LEU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 304 removed outlier: 4.178A pdb=" N ALA A 259 " --> pdb=" O GLY A 255 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA A 294 " --> pdb=" O ALA A 290 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN A 304 " --> pdb=" O ASP A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 311 removed outlier: 3.726A pdb=" N PHE A 311 " --> pdb=" O ALA A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 365 Processing helix chain 'A' and resid 366 through 368 No H-bonds generated for 'chain 'A' and resid 366 through 368' Processing helix chain 'A' and resid 371 through 387 removed outlier: 3.527A pdb=" N LEU A 375 " --> pdb=" O THR A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 412 removed outlier: 3.942A pdb=" N LEU A 392 " --> pdb=" O PRO A 388 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ARG A 397 " --> pdb=" O GLY A 393 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ASP A 398 " --> pdb=" O SER A 394 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LYS A 400 " --> pdb=" O TYR A 396 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N GLN A 401 " --> pdb=" O ARG A 397 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A 412 " --> pdb=" O THR A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 483 Processing helix chain 'A' and resid 504 through 510 Processing helix chain 'A' and resid 526 through 532 Processing helix chain 'A' and resid 538 through 549 Processing helix chain 'A' and resid 551 through 556 Processing helix chain 'A' and resid 574 through 590 Processing helix chain 'A' and resid 604 through 619 Processing helix chain 'A' and resid 632 through 636 Processing helix chain 'A' and resid 655 through 661 Processing helix chain 'A' and resid 665 through 691 removed outlier: 3.800A pdb=" N GLU A 669 " --> pdb=" O SER A 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 99 Processing helix chain 'B' and resid 104 through 140 removed outlier: 3.916A pdb=" N ARG B 108 " --> pdb=" O ASN B 104 " (cutoff:3.500A) Proline residue: B 129 - end of helix Processing helix chain 'B' and resid 151 through 199 removed outlier: 4.074A pdb=" N THR B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASN B 185 " --> pdb=" O LYS B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 209 removed outlier: 3.629A pdb=" N ARG B 209 " --> pdb=" O TRP B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 234 Processing helix chain 'B' and resid 236 through 254 removed outlier: 3.626A pdb=" N PHE B 254 " --> pdb=" O LEU B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 304 removed outlier: 4.179A pdb=" N ALA B 259 " --> pdb=" O GLY B 255 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA B 294 " --> pdb=" O ALA B 290 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN B 304 " --> pdb=" O ASP B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 311 removed outlier: 3.726A pdb=" N PHE B 311 " --> pdb=" O ALA B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 365 Processing helix chain 'B' and resid 366 through 368 No H-bonds generated for 'chain 'B' and resid 366 through 368' Processing helix chain 'B' and resid 371 through 387 removed outlier: 3.527A pdb=" N LEU B 375 " --> pdb=" O THR B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 412 removed outlier: 3.942A pdb=" N LEU B 392 " --> pdb=" O PRO B 388 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ARG B 397 " --> pdb=" O GLY B 393 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ASP B 398 " --> pdb=" O SER B 394 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LYS B 400 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N GLN B 401 " --> pdb=" O ARG B 397 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU B 412 " --> pdb=" O THR B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 483 Processing helix chain 'B' and resid 504 through 510 Processing helix chain 'B' and resid 526 through 532 Processing helix chain 'B' and resid 538 through 549 Processing helix chain 'B' and resid 551 through 556 Processing helix chain 'B' and resid 574 through 590 Processing helix chain 'B' and resid 604 through 619 Processing helix chain 'B' and resid 632 through 636 Processing helix chain 'B' and resid 655 through 661 Processing helix chain 'B' and resid 665 through 691 removed outlier: 3.800A pdb=" N GLU B 669 " --> pdb=" O SER B 665 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 438 through 439 Processing sheet with id=AA2, first strand: chain 'A' and resid 441 through 443 removed outlier: 7.148A pdb=" N PHE A 443 " --> pdb=" O LYS A 453 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N LYS A 453 " --> pdb=" O PHE A 443 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 512 through 515 removed outlier: 7.026A pdb=" N THR A 465 " --> pdb=" O TYR A 628 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ALA A 466 " --> pdb=" O ILE A 643 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LEU A 645 " --> pdb=" O ALA A 466 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL A 468 " --> pdb=" O LEU A 645 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 438 through 439 Processing sheet with id=AA5, first strand: chain 'B' and resid 441 through 443 removed outlier: 7.148A pdb=" N PHE B 443 " --> pdb=" O LYS B 453 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N LYS B 453 " --> pdb=" O PHE B 443 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 512 through 515 removed outlier: 7.026A pdb=" N THR B 465 " --> pdb=" O TYR B 628 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ALA B 466 " --> pdb=" O ILE B 643 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LEU B 645 " --> pdb=" O ALA B 466 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL B 468 " --> pdb=" O LEU B 645 " (cutoff:3.500A) 637 hydrogen bonds defined for protein. 1881 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.96 Time building geometry restraints manager: 2.96 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: 0.05 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: 0.010 Normalize map: mean=0, sd=1: 1.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 27.170 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 9788 Z= 0.418 Angle : 0.649 11.311 13226 Z= 0.342 Chirality : 0.040 0.194 1524 Planarity : 0.003 0.034 1664 Dihedral : 15.096 87.681 3650 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.22), residues: 1196 helix: -0.93 (0.17), residues: 778 sheet: -3.80 (0.67), residues: 56 loop : -4.02 (0.27), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 279 HIS 0.002 0.001 HIS B 656 PHE 0.012 0.001 PHE A 132 TYR 0.008 0.001 TYR B 310 ARG 0.002 0.000 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.826 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: 0.2759 time to fit residues: 47.9114 Evaluate side-chains 100 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN A 196 GLN A 346 GLN A 606 HIS B 127 GLN B 196 GLN B 346 GLN ** B 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 606 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.179048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.132037 restraints weight = 10183.628| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.54 r_work: 0.3396 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 9788 Z= 0.250 Angle : 0.561 7.533 13226 Z= 0.291 Chirality : 0.041 0.227 1524 Planarity : 0.004 0.035 1664 Dihedral : 8.194 56.750 1378 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.78 % Allowed : 10.56 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.24), residues: 1196 helix: 1.00 (0.18), residues: 780 sheet: -3.81 (0.66), residues: 56 loop : -3.08 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 279 HIS 0.005 0.001 HIS B 197 PHE 0.020 0.002 PHE A 132 TYR 0.032 0.002 TYR A 310 ARG 0.003 0.000 ARG B 632 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 126 time to evaluate : 1.021 Fit side-chains revert: symmetry clash REVERT: A 97 ARG cc_start: 0.8219 (ttp80) cc_final: 0.7902 (tmm160) REVERT: A 216 ARG cc_start: 0.6925 (ttp80) cc_final: 0.6634 (ttp80) REVERT: A 588 LEU cc_start: 0.7373 (mt) cc_final: 0.7064 (mp) REVERT: A 594 MET cc_start: 0.7642 (mmt) cc_final: 0.7198 (mmt) REVERT: A 662 MET cc_start: 0.6926 (mtp) cc_final: 0.6677 (ptp) REVERT: A 668 ARG cc_start: 0.8669 (mtp180) cc_final: 0.8209 (mtm180) REVERT: B 148 VAL cc_start: 0.8665 (p) cc_final: 0.8451 (m) REVERT: B 668 ARG cc_start: 0.8598 (mtp180) cc_final: 0.8118 (mtm180) outliers start: 8 outliers final: 6 residues processed: 131 average time/residue: 0.2466 time to fit residues: 44.0784 Evaluate side-chains 115 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 109 time to evaluate : 1.085 ------------------------------------------------------------------------------- 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 65 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 119 optimal weight: 20.0000 chunk 18 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 42 optimal weight: 0.0970 chunk 26 optimal weight: 0.8980 chunk 44 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 = 0.4047 r_free = 0.4047 target = 0.180172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.132695 restraints weight = 10331.007| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.57 r_work: 0.3400 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.2119 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= 0.189 Angle : 0.516 7.928 13226 Z= 0.266 Chirality : 0.039 0.239 1524 Planarity : 0.003 0.029 1664 Dihedral : 7.799 56.202 1378 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.36 % Allowed : 12.40 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.26), residues: 1196 helix: 1.66 (0.19), residues: 798 sheet: -3.76 (0.53), residues: 80 loop : -2.64 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 279 HIS 0.005 0.001 HIS A 606 PHE 0.020 0.001 PHE A 532 TYR 0.038 0.002 TYR B 310 ARG 0.006 0.000 ARG A 632 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 135 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 216 ARG cc_start: 0.6956 (ttp80) cc_final: 0.6567 (ttp80) REVERT: A 594 MET cc_start: 0.7519 (mmt) cc_final: 0.7254 (mmt) REVERT: A 668 ARG cc_start: 0.8679 (mtp180) cc_final: 0.8266 (mtm180) REVERT: B 97 ARG cc_start: 0.8165 (tmm160) cc_final: 0.7847 (ttp80) REVERT: B 148 VAL cc_start: 0.8682 (p) cc_final: 0.8411 (m) REVERT: B 216 ARG cc_start: 0.6963 (ttp80) cc_final: 0.6477 (ttp80) REVERT: B 668 ARG cc_start: 0.8647 (mtp180) cc_final: 0.8325 (mtp180) outliers start: 14 outliers final: 9 residues processed: 143 average time/residue: 0.2374 time to fit residues: 46.9692 Evaluate side-chains 128 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 119 time to evaluate : 1.073 ------------------------------------------------------------------------------- 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 116 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 54 optimal weight: 0.1980 chunk 77 optimal weight: 1.9990 chunk 40 optimal weight: 0.0870 chunk 1 optimal weight: 0.0970 chunk 115 optimal weight: 0.0980 chunk 47 optimal weight: 7.9990 chunk 59 optimal weight: 9.9990 chunk 46 optimal weight: 3.9990 overall best weight: 0.2156 ------------------------------------------------------------------------------- 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 = 0.4093 r_free = 0.4093 target = 0.184532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.138088 restraints weight = 10170.058| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.49 r_work: 0.3452 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9788 Z= 0.141 Angle : 0.491 8.206 13226 Z= 0.249 Chirality : 0.038 0.250 1524 Planarity : 0.003 0.027 1664 Dihedral : 7.345 57.258 1378 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.97 % Allowed : 14.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.26), residues: 1196 helix: 2.17 (0.19), residues: 790 sheet: -3.51 (0.55), residues: 80 loop : -1.91 (0.37), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 279 HIS 0.003 0.001 HIS A 606 PHE 0.019 0.001 PHE A 179 TYR 0.031 0.001 TYR B 310 ARG 0.006 0.000 ARG A 632 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 216 ARG cc_start: 0.6829 (ttp80) cc_final: 0.6399 (ttp80) REVERT: A 594 MET cc_start: 0.7310 (mmt) cc_final: 0.7098 (mmt) REVERT: A 668 ARG cc_start: 0.8663 (mtp180) cc_final: 0.8289 (mtm180) REVERT: B 97 ARG cc_start: 0.8024 (tmm160) cc_final: 0.7727 (ttp80) REVERT: B 148 VAL cc_start: 0.8625 (p) cc_final: 0.8362 (m) REVERT: B 216 ARG cc_start: 0.6793 (ttp80) cc_final: 0.6318 (ttp80) outliers start: 10 outliers final: 4 residues processed: 129 average time/residue: 0.2471 time to fit residues: 43.5083 Evaluate side-chains 117 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 113 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 659 LEU 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 46 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 111 optimal weight: 0.1980 chunk 34 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 113 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4062 r_free = 0.4062 target = 0.180982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.133394 restraints weight = 10284.273| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.54 r_work: 0.3380 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.2643 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= 0.196 Angle : 0.510 10.031 13226 Z= 0.257 Chirality : 0.039 0.255 1524 Planarity : 0.003 0.022 1664 Dihedral : 7.180 57.092 1378 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.26 % Allowed : 15.79 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.26), residues: 1196 helix: 2.20 (0.19), residues: 790 sheet: -3.35 (0.57), residues: 80 loop : -1.79 (0.37), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 279 HIS 0.003 0.001 HIS A 606 PHE 0.027 0.002 PHE B 254 TYR 0.019 0.001 TYR B 310 ARG 0.002 0.000 ARG A 616 *********************** 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 152 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 139 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 216 ARG cc_start: 0.7044 (ttp80) cc_final: 0.6604 (ttp80) REVERT: A 594 MET cc_start: 0.7465 (mmt) cc_final: 0.7242 (mmt) REVERT: A 668 ARG cc_start: 0.8664 (mtp180) cc_final: 0.8285 (mtm180) REVERT: B 97 ARG cc_start: 0.8127 (tmm160) cc_final: 0.7818 (ttp80) REVERT: B 148 VAL cc_start: 0.8669 (p) cc_final: 0.8392 (m) REVERT: B 216 ARG cc_start: 0.7018 (ttp80) cc_final: 0.6534 (ttp80) REVERT: B 594 MET cc_start: 0.7519 (mmt) cc_final: 0.7274 (mmt) REVERT: B 668 ARG cc_start: 0.8622 (mtp180) cc_final: 0.8342 (mtp180) outliers start: 13 outliers final: 7 residues processed: 150 average time/residue: 0.2343 time to fit residues: 48.8912 Evaluate side-chains 136 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 129 time to evaluate : 1.128 ------------------------------------------------------------------------------- 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 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 99 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 43 optimal weight: 0.0010 chunk 17 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 15 optimal weight: 0.4980 chunk 50 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 overall best weight: 0.8588 ------------------------------------------------------------------------------- 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 = 0.4040 r_free = 0.4040 target = 0.178706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.130184 restraints weight = 10405.274| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.51 r_work: 0.3360 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.2845 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= 0.218 Angle : 0.532 12.814 13226 Z= 0.265 Chirality : 0.039 0.237 1524 Planarity : 0.003 0.025 1664 Dihedral : 7.127 56.913 1378 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.87 % Allowed : 17.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.26), residues: 1196 helix: 2.17 (0.19), residues: 792 sheet: -3.24 (0.58), residues: 80 loop : -1.67 (0.37), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 279 HIS 0.002 0.001 HIS A 656 PHE 0.026 0.002 PHE A 254 TYR 0.016 0.002 TYR B 310 ARG 0.002 0.000 ARG B 632 *********************** 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: 9 poor density : 144 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 ARG cc_start: 0.6864 (ttp80) cc_final: 0.6365 (ttp80) REVERT: A 662 MET cc_start: 0.6441 (ptp) cc_final: 0.6224 (ptt) REVERT: A 668 ARG cc_start: 0.8676 (mtp180) cc_final: 0.8152 (mtp180) REVERT: B 97 ARG cc_start: 0.8072 (tmm160) cc_final: 0.7763 (ttp80) REVERT: B 148 VAL cc_start: 0.8586 (p) cc_final: 0.8322 (m) REVERT: B 216 ARG cc_start: 0.6882 (ttp80) cc_final: 0.6401 (ttp80) REVERT: B 662 MET cc_start: 0.6020 (ptp) cc_final: 0.5764 (ptp) REVERT: B 668 ARG cc_start: 0.8652 (mtp180) cc_final: 0.8367 (mtp180) outliers start: 9 outliers final: 6 residues processed: 151 average time/residue: 0.2246 time to fit residues: 47.2982 Evaluate side-chains 144 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 138 time to evaluate : 1.063 ------------------------------------------------------------------------------- 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 386 SER 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 23 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 = 0.3912 r_free = 0.3912 target = 0.165863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.116003 restraints weight = 10942.469| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.44 r_work: 0.3220 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.088 9788 Z= 0.568 Angle : 0.730 11.210 13226 Z= 0.377 Chirality : 0.048 0.257 1524 Planarity : 0.004 0.023 1664 Dihedral : 7.836 55.748 1378 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.94 % Allowed : 17.93 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.25), residues: 1196 helix: 1.26 (0.18), residues: 794 sheet: -3.33 (0.69), residues: 56 loop : -2.16 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 100 HIS 0.003 0.001 HIS A 197 PHE 0.039 0.003 PHE B 254 TYR 0.028 0.003 TYR A 269 ARG 0.003 0.000 ARG A 592 *********************** 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: 20 poor density : 132 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 VAL cc_start: 0.8642 (p) cc_final: 0.8400 (m) REVERT: A 216 ARG cc_start: 0.6795 (ttp80) cc_final: 0.6315 (ttp80) REVERT: A 668 ARG cc_start: 0.8625 (mtp180) cc_final: 0.8373 (ttm170) REVERT: B 97 ARG cc_start: 0.8229 (tmm160) cc_final: 0.7959 (ttp80) REVERT: B 148 VAL cc_start: 0.8579 (p) cc_final: 0.8312 (m) REVERT: B 216 ARG cc_start: 0.6787 (ttp80) cc_final: 0.6297 (ttp80) REVERT: B 594 MET cc_start: 0.7620 (mmt) cc_final: 0.7288 (mmt) REVERT: B 668 ARG cc_start: 0.8669 (mtp180) cc_final: 0.8248 (mtp180) outliers start: 20 outliers final: 17 residues processed: 141 average time/residue: 0.2271 time to fit residues: 44.4955 Evaluate side-chains 145 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 1.002 ------------------------------------------------------------------------------- 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 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 265 THR Chi-restraints excluded: chain B residue 312 ASN Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 408 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 5.9990 chunk 55 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 76 optimal weight: 0.7980 chunk 3 optimal weight: 0.0980 chunk 31 optimal weight: 0.8980 chunk 32 optimal weight: 0.1980 chunk 72 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.4029 r_free = 0.4029 target = 0.177499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.128629 restraints weight = 10628.421| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.51 r_work: 0.3336 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9788 Z= 0.177 Angle : 0.549 13.088 13226 Z= 0.274 Chirality : 0.038 0.199 1524 Planarity : 0.003 0.024 1664 Dihedral : 7.432 56.303 1378 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.74 % Allowed : 18.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.26), residues: 1196 helix: 1.93 (0.19), residues: 796 sheet: -3.22 (0.58), residues: 80 loop : -1.75 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 279 HIS 0.002 0.001 HIS A 656 PHE 0.021 0.001 PHE A 254 TYR 0.021 0.001 TYR A 310 ARG 0.002 0.000 ARG B 632 *********************** 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: 18 poor density : 134 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 216 ARG cc_start: 0.6859 (ttp80) cc_final: 0.6399 (ttp80) REVERT: A 481 LEU cc_start: 0.7780 (tp) cc_final: 0.7205 (mp) REVERT: A 594 MET cc_start: 0.7641 (mmt) cc_final: 0.7124 (mmt) REVERT: A 668 ARG cc_start: 0.8659 (mtp180) cc_final: 0.8247 (mtp180) REVERT: B 148 VAL cc_start: 0.8660 (p) cc_final: 0.8408 (m) REVERT: B 216 ARG cc_start: 0.6884 (ttp80) cc_final: 0.6391 (ttp80) REVERT: B 481 LEU cc_start: 0.7810 (tp) cc_final: 0.7255 (mp) REVERT: B 668 ARG cc_start: 0.8671 (mtp180) cc_final: 0.8351 (mtp180) outliers start: 18 outliers final: 11 residues processed: 145 average time/residue: 0.2373 time to fit residues: 47.8718 Evaluate side-chains 140 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 390 ASN Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain B residue 156 LEU 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 27 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 89 optimal weight: 0.0060 chunk 7 optimal weight: 0.9990 chunk 32 optimal weight: 0.1980 chunk 116 optimal weight: 6.9990 chunk 70 optimal weight: 0.0870 chunk 113 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 overall best weight: 0.4176 ------------------------------------------------------------------------------- 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 = 0.4027 r_free = 0.4027 target = 0.177556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.128689 restraints weight = 10533.209| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.58 r_work: 0.3356 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9788 Z= 0.167 Angle : 0.556 13.980 13226 Z= 0.269 Chirality : 0.038 0.204 1524 Planarity : 0.003 0.024 1664 Dihedral : 7.150 58.659 1378 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.16 % Allowed : 20.54 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.26), residues: 1196 helix: 2.28 (0.19), residues: 790 sheet: -3.18 (0.58), residues: 80 loop : -1.42 (0.37), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 279 HIS 0.004 0.001 HIS A 656 PHE 0.012 0.001 PHE A 438 TYR 0.022 0.001 TYR A 310 ARG 0.002 0.000 ARG B 165 *********************** 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 141 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 129 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 ARG cc_start: 0.6987 (ttp80) cc_final: 0.6528 (ttp80) REVERT: A 594 MET cc_start: 0.7629 (mmt) cc_final: 0.7197 (mmt) REVERT: A 668 ARG cc_start: 0.8677 (mtp180) cc_final: 0.8259 (mtp180) REVERT: B 97 ARG cc_start: 0.8047 (tmm160) cc_final: 0.7720 (ttp80) REVERT: B 148 VAL cc_start: 0.8703 (p) cc_final: 0.8431 (m) REVERT: B 216 ARG cc_start: 0.7009 (ttp80) cc_final: 0.6515 (ttp80) outliers start: 12 outliers final: 11 residues processed: 136 average time/residue: 0.2315 time to fit residues: 43.9797 Evaluate side-chains 135 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 124 time to evaluate : 1.074 ------------------------------------------------------------------------------- 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 477 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 119 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 32 optimal weight: 0.2980 chunk 59 optimal weight: 8.9990 chunk 48 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3997 r_free = 0.3997 target = 0.174415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.124978 restraints weight = 10642.357| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.56 r_work: 0.3317 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.3283 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= 0.247 Angle : 0.586 11.319 13226 Z= 0.288 Chirality : 0.040 0.219 1524 Planarity : 0.003 0.023 1664 Dihedral : 7.178 59.056 1378 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.16 % Allowed : 20.54 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.26), residues: 1196 helix: 2.23 (0.19), residues: 790 sheet: -3.24 (0.58), residues: 80 loop : -1.43 (0.37), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 279 HIS 0.002 0.001 HIS A 656 PHE 0.021 0.002 PHE B 443 TYR 0.018 0.002 TYR A 310 ARG 0.001 0.000 ARG B 585 ********************** 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 139 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 127 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 ARG cc_start: 0.6992 (ttp80) cc_final: 0.6515 (ttp80) REVERT: A 668 ARG cc_start: 0.8640 (mtp180) cc_final: 0.8306 (mtp180) REVERT: B 97 ARG cc_start: 0.8065 (tmm160) cc_final: 0.7745 (ttp80) REVERT: B 148 VAL cc_start: 0.8727 (p) cc_final: 0.8466 (m) REVERT: B 216 ARG cc_start: 0.7026 (ttp80) cc_final: 0.6530 (ttp80) REVERT: B 659 LEU cc_start: 0.5178 (OUTLIER) cc_final: 0.4939 (tp) outliers start: 12 outliers final: 11 residues processed: 134 average time/residue: 0.2391 time to fit residues: 45.0633 Evaluate side-chains 138 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 1.063 ------------------------------------------------------------------------------- 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 477 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 B residue 156 LEU 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 110 optimal weight: 0.4980 chunk 116 optimal weight: 7.9990 chunk 63 optimal weight: 0.1980 chunk 96 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 87 optimal weight: 0.0980 chunk 82 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 111 optimal weight: 0.0970 chunk 28 optimal weight: 0.6980 overall best weight: 0.3178 ------------------------------------------------------------------------------- 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 = 0.4076 r_free = 0.4076 target = 0.182398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.134793 restraints weight = 10375.366| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.56 r_work: 0.3410 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9788 Z= 0.157 Angle : 0.544 10.157 13226 Z= 0.265 Chirality : 0.038 0.220 1524 Planarity : 0.003 0.022 1664 Dihedral : 7.011 58.650 1378 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.07 % Allowed : 20.54 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.26), residues: 1196 helix: 2.49 (0.18), residues: 790 sheet: -3.15 (0.58), residues: 80 loop : -1.41 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 279 HIS 0.002 0.001 HIS A 656 PHE 0.020 0.001 PHE B 443 TYR 0.015 0.001 TYR A 310 ARG 0.002 0.000 ARG B 165 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4272.94 seconds wall clock time: 76 minutes 36.14 seconds (4596.14 seconds total)