Starting phenix.real_space_refine on Sun Nov 17 06:40:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fy5_29553/11_2024/8fy5_29553.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fy5_29553/11_2024/8fy5_29553.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fy5_29553/11_2024/8fy5_29553.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fy5_29553/11_2024/8fy5_29553.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fy5_29553/11_2024/8fy5_29553.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fy5_29553/11_2024/8fy5_29553.cif" } resolution = 3.5 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= 0.004 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 S 38 5.16 5 C 4244 2.51 5 N 1086 2.21 5 O 1080 1.98 5 H 6754 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 13202 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 6163 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 16, 'TRANS': 370} Chain breaks: 1 Chain: "B" Number of atoms: 6163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 6163 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 16, 'TRANS': 370} Chain breaks: 1 Chain: "C" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 438 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 1, 'TRANS': 26} Chain: "D" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 438 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 1, 'TRANS': 26} Time building chain proxies: 7.12, per 1000 atoms: 0.54 Number of scatterers: 13202 At special positions: 0 Unit cell: (107.07, 75.53, 80.51, 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 38 16.00 O 1080 8.00 N 1086 7.00 C 4244 6.00 H 6754 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.93 Conformation dependent library (CDL) restraints added in 1.1 seconds 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1576 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 2 sheets defined 90.4% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 33 through 50 removed outlier: 3.593A pdb=" N ILE A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 57 removed outlier: 4.047A pdb=" N VAL A 55 " --> pdb=" O MET A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 102 removed outlier: 4.806A pdb=" N ARG A 72 " --> pdb=" O ARG A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 121 Processing helix chain 'A' and resid 122 through 133 Processing helix chain 'A' and resid 136 through 164 removed outlier: 4.299A pdb=" N ILE A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 168 Processing helix chain 'A' and resid 169 through 175 Processing helix chain 'A' and resid 177 through 190 removed outlier: 3.645A pdb=" N TYR A 181 " --> pdb=" O HIS A 177 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG A 183 " --> pdb=" O ALA A 179 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL A 185 " --> pdb=" O TYR A 181 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N LEU A 186 " --> pdb=" O ARG A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 274 Processing helix chain 'A' and resid 274 through 284 removed outlier: 3.556A pdb=" N LEU A 278 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASP A 279 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE A 280 " --> pdb=" O LEU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 295 Processing helix chain 'A' and resid 298 through 333 Proline residue: A 308 - end of helix removed outlier: 3.862A pdb=" N HIS A 333 " --> pdb=" O SER A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 353 Processing helix chain 'A' and resid 354 through 364 Processing helix chain 'A' and resid 368 through 399 removed outlier: 3.809A pdb=" N GLU A 372 " --> pdb=" O GLN A 368 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU A 373 " --> pdb=" O PRO A 369 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLU A 374 " --> pdb=" O ARG A 370 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N PHE A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLN A 390 " --> pdb=" O ALA A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 405 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 415 through 440 removed outlier: 4.878A pdb=" N TYR A 426 " --> pdb=" O LYS A 422 " (cutoff:3.500A) Proline residue: A 427 - end of helix removed outlier: 3.874A pdb=" N CYS A 438 " --> pdb=" O PHE A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 461 Proline residue: A 456 - end of helix Processing helix chain 'A' and resid 461 through 476 removed outlier: 3.824A pdb=" N ARG A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL A 475 " --> pdb=" O ALA A 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 50 removed outlier: 3.589A pdb=" N ILE B 46 " --> pdb=" O ALA B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 57 removed outlier: 4.089A pdb=" N VAL B 55 " --> pdb=" O MET B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 102 removed outlier: 4.689A pdb=" N ARG B 72 " --> pdb=" O ARG B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 121 Processing helix chain 'B' and resid 122 through 133 Processing helix chain 'B' and resid 136 through 164 removed outlier: 4.319A pdb=" N ILE B 140 " --> pdb=" O VAL B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 168 Processing helix chain 'B' and resid 169 through 175 Processing helix chain 'B' and resid 177 through 190 removed outlier: 3.561A pdb=" N TYR B 181 " --> pdb=" O HIS B 177 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG B 183 " --> pdb=" O ALA B 179 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N VAL B 185 " --> pdb=" O TYR B 181 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N LEU B 186 " --> pdb=" O ARG B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 274 Processing helix chain 'B' and resid 274 through 284 removed outlier: 3.569A pdb=" N LEU B 278 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASP B 279 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE B 280 " --> pdb=" O LEU B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 295 Processing helix chain 'B' and resid 298 through 333 Proline residue: B 308 - end of helix removed outlier: 3.867A pdb=" N HIS B 333 " --> pdb=" O SER B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 353 Processing helix chain 'B' and resid 354 through 364 Processing helix chain 'B' and resid 368 through 370 No H-bonds generated for 'chain 'B' and resid 368 through 370' Processing helix chain 'B' and resid 371 through 399 removed outlier: 3.839A pdb=" N PHE B 389 " --> pdb=" O LEU B 385 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLN B 390 " --> pdb=" O ALA B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 405 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 415 through 440 removed outlier: 4.863A pdb=" N TYR B 426 " --> pdb=" O LYS B 422 " (cutoff:3.500A) Proline residue: B 427 - end of helix removed outlier: 3.732A pdb=" N CYS B 438 " --> pdb=" O PHE B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 461 removed outlier: 3.570A pdb=" N ILE B 453 " --> pdb=" O HIS B 449 " (cutoff:3.500A) Proline residue: B 456 - end of helix Processing helix chain 'B' and resid 461 through 476 removed outlier: 3.904A pdb=" N VAL B 475 " --> pdb=" O ALA B 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 410 Processing helix chain 'D' and resid 384 through 410 Processing sheet with id=AA1, first strand: chain 'A' and resid 255 through 256 removed outlier: 4.234A pdb=" N ALA A 337 " --> pdb=" O LEU A 256 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 255 through 256 removed outlier: 4.296A pdb=" N ALA B 337 " --> pdb=" O LEU B 256 " (cutoff:3.500A) 520 hydrogen bonds defined for protein. 1542 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: 4.80 Time building geometry restraints manager: 4.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6736 1.03 - 1.23: 19 1.23 - 1.42: 2681 1.42 - 1.61: 3852 1.61 - 1.81: 58 Bond restraints: 13346 Sorted by residual: bond pdb=" CB PRO B 369 " pdb=" CG PRO B 369 " ideal model delta sigma weight residual 1.492 1.610 -0.118 5.00e-02 4.00e+02 5.53e+00 bond pdb=" N LEU D 383 " pdb=" CA LEU D 383 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.98e+00 bond pdb=" N LEU C 383 " pdb=" CA LEU C 383 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.87e+00 bond pdb=" N ILE A 30 " pdb=" CA ILE A 30 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.71e+00 bond pdb=" N ILE B 30 " pdb=" CA ILE B 30 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.71e+00 ... (remaining 13341 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 23942 1.78 - 3.56: 211 3.56 - 5.34: 45 5.34 - 7.12: 3 7.12 - 8.89: 1 Bond angle restraints: 24202 Sorted by residual: angle pdb=" CA PRO B 369 " pdb=" N PRO B 369 " pdb=" CD PRO B 369 " ideal model delta sigma weight residual 112.00 103.11 8.89 1.40e+00 5.10e-01 4.04e+01 angle pdb=" N VAL A 475 " pdb=" CA VAL A 475 " pdb=" C VAL A 475 " ideal model delta sigma weight residual 111.90 108.05 3.85 8.10e-01 1.52e+00 2.26e+01 angle pdb=" N ARG A 474 " pdb=" CA ARG A 474 " pdb=" C ARG A 474 " ideal model delta sigma weight residual 114.56 109.40 5.16 1.27e+00 6.20e-01 1.65e+01 angle pdb=" N ARG B 474 " pdb=" CA ARG B 474 " pdb=" C ARG B 474 " ideal model delta sigma weight residual 114.56 109.56 5.00 1.27e+00 6.20e-01 1.55e+01 angle pdb=" C LEU D 383 " pdb=" N ILE D 384 " pdb=" CA ILE D 384 " ideal model delta sigma weight residual 120.24 122.19 -1.95 6.30e-01 2.52e+00 9.61e+00 ... (remaining 24197 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 5593 17.44 - 34.88: 440 34.88 - 52.31: 159 52.31 - 69.75: 49 69.75 - 87.19: 7 Dihedral angle restraints: 6248 sinusoidal: 3352 harmonic: 2896 Sorted by residual: dihedral pdb=" CA LEU A 276 " pdb=" C LEU A 276 " pdb=" N ILE A 277 " pdb=" CA ILE A 277 " ideal model delta harmonic sigma weight residual 180.00 160.16 19.84 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA LEU B 276 " pdb=" C LEU B 276 " pdb=" N ILE B 277 " pdb=" CA ILE B 277 " ideal model delta harmonic sigma weight residual 180.00 160.26 19.74 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA PHE B 99 " pdb=" C PHE B 99 " pdb=" N GLN B 100 " pdb=" CA GLN B 100 " ideal model delta harmonic sigma weight residual 180.00 161.33 18.67 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 6245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 751 0.030 - 0.060: 235 0.060 - 0.090: 85 0.090 - 0.120: 31 0.120 - 0.150: 4 Chirality restraints: 1106 Sorted by residual: chirality pdb=" CA ILE A 30 " pdb=" N ILE A 30 " pdb=" C ILE A 30 " pdb=" CB ILE A 30 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.63e-01 chirality pdb=" CA ILE B 30 " pdb=" N ILE B 30 " pdb=" C ILE B 30 " pdb=" CB ILE B 30 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.71e-01 chirality pdb=" CA PRO B 165 " pdb=" N PRO B 165 " pdb=" C PRO B 165 " pdb=" CB PRO B 165 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.78e-01 ... (remaining 1103 not shown) Planarity restraints: 1888 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN B 368 " 0.094 5.00e-02 4.00e+02 1.37e-01 2.99e+01 pdb=" N PRO B 369 " -0.236 5.00e-02 4.00e+02 pdb=" CA PRO B 369 " 0.071 5.00e-02 4.00e+02 pdb=" CD PRO B 369 " 0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 164 " 0.045 5.00e-02 4.00e+02 6.88e-02 7.58e+00 pdb=" N PRO A 165 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO A 165 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 165 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 164 " -0.042 5.00e-02 4.00e+02 6.43e-02 6.61e+00 pdb=" N PRO B 165 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO B 165 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 165 " -0.036 5.00e-02 4.00e+02 ... (remaining 1885 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.22: 1114 2.22 - 2.81: 29180 2.81 - 3.41: 37859 3.41 - 4.00: 48357 4.00 - 4.60: 76251 Nonbonded interactions: 192761 Sorted by model distance: nonbonded pdb=" O PHE A 434 " pdb=" HG1 THR A 437 " model vdw 1.625 2.450 nonbonded pdb=" O GLN A 173 " pdb="HH21 ARG A 178 " model vdw 1.672 2.450 nonbonded pdb=" O ALA A 364 " pdb="HH12 ARG A 375 " model vdw 1.676 2.450 nonbonded pdb=" O PHE B 434 " pdb=" HG1 THR B 437 " model vdw 1.693 2.450 nonbonded pdb=" OD1 ASP A 290 " pdb="HH12 ARG A 294 " model vdw 1.705 2.450 ... (remaining 192756 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.220 Extract box with map and model: 0.580 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 32.250 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 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 : 0.004 0.118 6592 Z= 0.242 Angle : 0.607 8.894 8974 Z= 0.356 Chirality : 0.036 0.150 1106 Planarity : 0.006 0.137 1098 Dihedral : 14.569 85.695 2318 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.00 % Allowed : 13.36 % Favored : 86.64 % 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: 2.45 (0.31), residues: 818 helix: 1.96 (0.20), residues: 694 sheet: None (None), residues: 0 loop : -0.22 (0.66), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 324 HIS 0.005 0.001 HIS A 328 PHE 0.014 0.001 PHE A 448 TYR 0.008 0.001 TYR B 426 ARG 0.002 0.000 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 1.102 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.4300 time to fit residues: 51.6037 Evaluate side-chains 87 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 40 optimal weight: 0.0770 chunk 32 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 overall best weight: 1.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.0616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6592 Z= 0.249 Angle : 0.564 5.783 8974 Z= 0.301 Chirality : 0.036 0.135 1106 Planarity : 0.005 0.076 1098 Dihedral : 4.237 20.579 890 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.58 % Allowed : 12.21 % Favored : 86.21 % 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: 2.46 (0.30), residues: 818 helix: 2.04 (0.20), residues: 696 sheet: None (None), residues: 0 loop : -0.78 (0.59), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 324 HIS 0.006 0.001 HIS B 328 PHE 0.011 0.001 PHE A 448 TYR 0.008 0.002 TYR A 359 ARG 0.002 0.000 ARG B 178 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 1.035 Fit side-chains revert: symmetry clash REVERT: B 464 LEU cc_start: 0.8806 (tt) cc_final: 0.8557 (mp) REVERT: B 468 LEU cc_start: 0.6829 (tt) cc_final: 0.6322 (mp) outliers start: 11 outliers final: 6 residues processed: 100 average time/residue: 0.4422 time to fit residues: 58.5202 Evaluate side-chains 95 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain D residue 386 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6592 Z= 0.209 Angle : 0.524 5.812 8974 Z= 0.276 Chirality : 0.035 0.122 1106 Planarity : 0.005 0.060 1098 Dihedral : 4.130 19.933 890 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.01 % Allowed : 12.64 % Favored : 86.35 % 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: 2.68 (0.30), residues: 818 helix: 2.18 (0.20), residues: 700 sheet: None (None), residues: 0 loop : -0.75 (0.60), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 324 HIS 0.006 0.001 HIS B 328 PHE 0.009 0.001 PHE A 434 TYR 0.009 0.002 TYR A 313 ARG 0.002 0.000 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 1.096 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.6233 (OUTLIER) cc_final: 0.4701 (mm-40) REVERT: B 284 ASN cc_start: 0.7889 (t0) cc_final: 0.7391 (t0) REVERT: B 464 LEU cc_start: 0.8773 (tt) cc_final: 0.8530 (mp) REVERT: B 468 LEU cc_start: 0.6782 (tt) cc_final: 0.6284 (mp) outliers start: 7 outliers final: 5 residues processed: 93 average time/residue: 0.4255 time to fit residues: 52.9746 Evaluate side-chains 91 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain D residue 386 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6592 Z= 0.211 Angle : 0.517 5.840 8974 Z= 0.272 Chirality : 0.035 0.125 1106 Planarity : 0.004 0.054 1098 Dihedral : 4.038 19.387 890 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.58 % Allowed : 12.64 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.71 (0.30), residues: 818 helix: 2.22 (0.20), residues: 700 sheet: None (None), residues: 0 loop : -0.85 (0.59), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 324 HIS 0.005 0.001 HIS B 328 PHE 0.010 0.001 PHE A 434 TYR 0.008 0.002 TYR A 313 ARG 0.002 0.000 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 1.119 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.6396 (OUTLIER) cc_final: 0.4922 (mm-40) REVERT: A 76 THR cc_start: 0.8485 (m) cc_final: 0.8255 (p) REVERT: B 464 LEU cc_start: 0.8769 (tt) cc_final: 0.8535 (mp) REVERT: B 468 LEU cc_start: 0.6802 (tt) cc_final: 0.6308 (mp) outliers start: 11 outliers final: 8 residues processed: 91 average time/residue: 0.4470 time to fit residues: 53.6557 Evaluate side-chains 87 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain D residue 386 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 0 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 69 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6592 Z= 0.210 Angle : 0.513 5.874 8974 Z= 0.270 Chirality : 0.035 0.123 1106 Planarity : 0.004 0.054 1098 Dihedral : 4.047 19.338 890 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.30 % Allowed : 11.35 % Favored : 86.35 % 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: 2.75 (0.30), residues: 818 helix: 2.26 (0.20), residues: 700 sheet: None (None), residues: 0 loop : -0.91 (0.59), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 324 HIS 0.005 0.001 HIS B 328 PHE 0.010 0.001 PHE A 434 TYR 0.008 0.002 TYR A 313 ARG 0.002 0.000 ARG A 367 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 1.124 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.6386 (OUTLIER) cc_final: 0.4955 (mm-40) REVERT: A 76 THR cc_start: 0.8497 (OUTLIER) cc_final: 0.8277 (p) REVERT: B 464 LEU cc_start: 0.8771 (tt) cc_final: 0.8540 (mp) REVERT: B 468 LEU cc_start: 0.6760 (tt) cc_final: 0.6274 (mp) outliers start: 16 outliers final: 11 residues processed: 93 average time/residue: 0.4154 time to fit residues: 51.9600 Evaluate side-chains 93 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain D residue 386 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 1.9990 chunk 15 optimal weight: 9.9990 chunk 45 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 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 0.028 6592 Z= 0.189 Angle : 0.503 5.868 8974 Z= 0.264 Chirality : 0.035 0.122 1106 Planarity : 0.004 0.051 1098 Dihedral : 3.977 18.754 890 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.73 % Allowed : 10.49 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.86 (0.30), residues: 818 helix: 2.34 (0.20), residues: 702 sheet: None (None), residues: 0 loop : -0.95 (0.59), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 324 HIS 0.005 0.001 HIS A 328 PHE 0.009 0.001 PHE A 434 TYR 0.008 0.001 TYR A 313 ARG 0.002 0.000 ARG B 294 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 1.191 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.6455 (OUTLIER) cc_final: 0.5046 (mm-40) REVERT: A 76 THR cc_start: 0.8469 (m) cc_final: 0.8248 (p) REVERT: A 352 VAL cc_start: 0.8645 (OUTLIER) cc_final: 0.8434 (t) REVERT: A 426 TYR cc_start: 0.9263 (OUTLIER) cc_final: 0.9060 (m-80) REVERT: B 464 LEU cc_start: 0.8763 (tt) cc_final: 0.8536 (mp) REVERT: B 468 LEU cc_start: 0.6829 (tt) cc_final: 0.6363 (mp) outliers start: 19 outliers final: 10 residues processed: 97 average time/residue: 0.4130 time to fit residues: 53.8706 Evaluate side-chains 94 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain D residue 386 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 48 optimal weight: 0.0980 chunk 47 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6592 Z= 0.171 Angle : 0.499 5.863 8974 Z= 0.260 Chirality : 0.035 0.131 1106 Planarity : 0.004 0.050 1098 Dihedral : 3.921 18.252 890 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.87 % Allowed : 11.78 % Favored : 86.35 % 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: 2.97 (0.30), residues: 818 helix: 2.41 (0.20), residues: 702 sheet: None (None), residues: 0 loop : -0.94 (0.60), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 324 HIS 0.005 0.001 HIS A 328 PHE 0.009 0.001 PHE A 434 TYR 0.008 0.001 TYR A 313 ARG 0.005 0.000 ARG C 407 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.985 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.6415 (OUTLIER) cc_final: 0.5009 (mm-40) REVERT: A 352 VAL cc_start: 0.8630 (OUTLIER) cc_final: 0.8415 (t) REVERT: A 426 TYR cc_start: 0.9260 (OUTLIER) cc_final: 0.9050 (m-80) REVERT: B 464 LEU cc_start: 0.8751 (tt) cc_final: 0.8540 (mp) REVERT: B 468 LEU cc_start: 0.6819 (tt) cc_final: 0.6354 (mp) outliers start: 13 outliers final: 8 residues processed: 90 average time/residue: 0.4028 time to fit residues: 48.7473 Evaluate side-chains 89 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 363 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 9.9990 chunk 14 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6592 Z= 0.234 Angle : 0.516 5.913 8974 Z= 0.271 Chirality : 0.036 0.123 1106 Planarity : 0.004 0.049 1098 Dihedral : 3.946 19.051 890 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.58 % Allowed : 12.21 % Favored : 86.21 % 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: 2.88 (0.30), residues: 818 helix: 2.35 (0.20), residues: 702 sheet: None (None), residues: 0 loop : -0.98 (0.59), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 324 HIS 0.005 0.001 HIS A 328 PHE 0.010 0.001 PHE A 434 TYR 0.008 0.001 TYR A 359 ARG 0.004 0.000 ARG A 72 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 1.085 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.6514 (OUTLIER) cc_final: 0.5125 (mm-40) REVERT: A 352 VAL cc_start: 0.8671 (OUTLIER) cc_final: 0.8459 (t) REVERT: A 426 TYR cc_start: 0.9277 (OUTLIER) cc_final: 0.9059 (m-80) REVERT: B 468 LEU cc_start: 0.6867 (tt) cc_final: 0.6378 (mp) outliers start: 11 outliers final: 8 residues processed: 92 average time/residue: 0.4410 time to fit residues: 55.0247 Evaluate side-chains 93 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 363 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6592 Z= 0.202 Angle : 0.506 5.862 8974 Z= 0.264 Chirality : 0.035 0.122 1106 Planarity : 0.004 0.049 1098 Dihedral : 3.916 18.728 890 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.58 % Allowed : 12.79 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.98 (0.30), residues: 818 helix: 2.42 (0.20), residues: 702 sheet: None (None), residues: 0 loop : -1.01 (0.60), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 324 HIS 0.004 0.001 HIS A 328 PHE 0.009 0.001 PHE A 434 TYR 0.008 0.001 TYR B 313 ARG 0.003 0.000 ARG A 72 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 1.010 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.6360 (OUTLIER) cc_final: 0.5022 (mm-40) REVERT: A 352 VAL cc_start: 0.8655 (OUTLIER) cc_final: 0.8445 (t) REVERT: A 426 TYR cc_start: 0.9272 (OUTLIER) cc_final: 0.9067 (m-80) REVERT: A 464 LEU cc_start: 0.8852 (tt) cc_final: 0.8626 (mp) REVERT: B 468 LEU cc_start: 0.6797 (tt) cc_final: 0.6380 (mp) outliers start: 11 outliers final: 8 residues processed: 91 average time/residue: 0.4197 time to fit residues: 51.1760 Evaluate side-chains 92 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 363 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 0.4980 chunk 52 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 67 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6592 Z= 0.187 Angle : 0.505 5.853 8974 Z= 0.263 Chirality : 0.035 0.121 1106 Planarity : 0.004 0.048 1098 Dihedral : 3.876 18.459 890 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.58 % Allowed : 12.79 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.08 (0.30), residues: 818 helix: 2.50 (0.20), residues: 702 sheet: None (None), residues: 0 loop : -1.01 (0.60), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 324 HIS 0.004 0.001 HIS A 328 PHE 0.009 0.001 PHE A 434 TYR 0.008 0.001 TYR A 313 ARG 0.004 0.000 ARG B 309 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 1.151 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.6427 (OUTLIER) cc_final: 0.5095 (mm-40) REVERT: A 352 VAL cc_start: 0.8641 (OUTLIER) cc_final: 0.8428 (t) REVERT: A 426 TYR cc_start: 0.9279 (OUTLIER) cc_final: 0.9070 (m-80) REVERT: A 464 LEU cc_start: 0.8857 (tt) cc_final: 0.8626 (mp) REVERT: B 468 LEU cc_start: 0.6781 (tt) cc_final: 0.6377 (mp) outliers start: 11 outliers final: 7 residues processed: 91 average time/residue: 0.4333 time to fit residues: 52.9051 Evaluate side-chains 93 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 363 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.134600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.099607 restraints weight = 22971.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.102209 restraints weight = 17797.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.103973 restraints weight = 15268.582| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6592 Z= 0.247 Angle : 0.528 5.922 8974 Z= 0.275 Chirality : 0.036 0.123 1106 Planarity : 0.004 0.049 1098 Dihedral : 3.927 19.418 890 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.72 % Allowed : 12.93 % Favored : 85.34 % 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: 2.94 (0.30), residues: 818 helix: 2.39 (0.20), residues: 702 sheet: None (None), residues: 0 loop : -0.98 (0.60), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 324 HIS 0.005 0.001 HIS B 328 PHE 0.011 0.001 PHE A 99 TYR 0.008 0.002 TYR A 313 ARG 0.002 0.000 ARG A 72 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3104.93 seconds wall clock time: 56 minutes 12.53 seconds (3372.53 seconds total)