Starting phenix.real_space_refine on Sat Dec 28 11:30:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uvf_42618/12_2024/8uvf_42618.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uvf_42618/12_2024/8uvf_42618.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uvf_42618/12_2024/8uvf_42618.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uvf_42618/12_2024/8uvf_42618.map" model { file = "/net/cci-nas-00/data/ceres_data/8uvf_42618/12_2024/8uvf_42618.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uvf_42618/12_2024/8uvf_42618.cif" } resolution = 2.17 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= 0.001 sd= 0.042 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: 6 Type Number sf(0) Gaussians P 4 5.49 5 S 52 5.16 5 Na 4 4.78 5 C 5818 2.51 5 N 1272 2.21 5 O 1370 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 8520 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 4011 Classifications: {'peptide': 513} Link IDs: {'PTRANS': 34, 'TRANS': 478} Chain breaks: 2 Chain: "A" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 249 Unusual residues: {' NA': 2, '3PE': 2, 'C14': 3, 'CLR': 4} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Restraints were copied for chains: B Time building chain proxies: 8.47, per 1000 atoms: 0.99 Number of scatterers: 8520 At special positions: 0 Unit cell: (84.975, 110.55, 82.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 52 16.00 P 4 15.00 Na 4 11.00 O 1370 8.00 N 1272 7.00 C 5818 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: 2.61 Conformation dependent library (CDL) restraints added in 996.1 milliseconds 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1924 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 0 sheets defined 84.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 1 through 14 removed outlier: 3.614A pdb=" N ALA A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 34 Proline residue: A 24 - end of helix Proline residue: A 29 - end of helix removed outlier: 3.884A pdb=" N PHE A 32 " --> pdb=" O LEU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 54 Processing helix chain 'A' and resid 58 through 64 Processing helix chain 'A' and resid 64 through 73 removed outlier: 3.751A pdb=" N VAL A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Proline residue: A 71 - end of helix Processing helix chain 'A' and resid 77 through 82 Processing helix chain 'A' and resid 83 through 86 Processing helix chain 'A' and resid 87 through 106 removed outlier: 3.676A pdb=" N PHE A 91 " --> pdb=" O LEU A 87 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TRP A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 121 removed outlier: 3.613A pdb=" N GLY A 121 " --> pdb=" O LEU A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 140 Processing helix chain 'A' and resid 143 through 163 Proline residue: A 153 - end of helix Processing helix chain 'A' and resid 220 through 247 removed outlier: 3.656A pdb=" N ILE A 238 " --> pdb=" O PHE A 234 " (cutoff:3.500A) Proline residue: A 239 - end of helix removed outlier: 3.834A pdb=" N THR A 247 " --> pdb=" O SER A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 267 removed outlier: 3.989A pdb=" N LEU A 257 " --> pdb=" O THR A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 301 Proline residue: A 284 - end of helix Processing helix chain 'A' and resid 320 through 335 Processing helix chain 'A' and resid 339 through 359 Processing helix chain 'A' and resid 366 through 371 Processing helix chain 'A' and resid 377 through 390 removed outlier: 3.796A pdb=" N ILE A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU A 389 " --> pdb=" O ILE A 385 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N PHE A 390 " --> pdb=" O VAL A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 404 removed outlier: 3.907A pdb=" N PHE A 403 " --> pdb=" O LEU A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 425 Processing helix chain 'A' and resid 426 through 446 Processing helix chain 'A' and resid 447 through 456 Processing helix chain 'A' and resid 457 through 460 Processing helix chain 'A' and resid 463 through 479 Processing helix chain 'A' and resid 483 through 503 Proline residue: A 493 - end of helix Processing helix chain 'A' and resid 505 through 517 removed outlier: 3.833A pdb=" N LEU A 509 " --> pdb=" O HIS A 505 " (cutoff:3.500A) Proline residue: A 512 - end of helix Processing helix chain 'A' and resid 527 through 535 Processing helix chain 'A' and resid 540 through 566 removed outlier: 4.198A pdb=" N LEU A 550 " --> pdb=" O ARG A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 572 Processing helix chain 'A' and resid 577 through 581 Processing helix chain 'B' and resid 2 through 14 Processing helix chain 'B' and resid 14 through 34 Proline residue: B 24 - end of helix Proline residue: B 29 - end of helix removed outlier: 3.883A pdb=" N PHE B 32 " --> pdb=" O LEU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 54 Processing helix chain 'B' and resid 58 through 64 Processing helix chain 'B' and resid 64 through 73 removed outlier: 3.750A pdb=" N VAL B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) Proline residue: B 71 - end of helix Processing helix chain 'B' and resid 77 through 82 Processing helix chain 'B' and resid 83 through 86 Processing helix chain 'B' and resid 87 through 106 removed outlier: 3.676A pdb=" N PHE B 91 " --> pdb=" O LEU B 87 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TRP B 106 " --> pdb=" O ALA B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 121 removed outlier: 3.614A pdb=" N GLY B 121 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 140 Processing helix chain 'B' and resid 143 through 163 Proline residue: B 153 - end of helix Processing helix chain 'B' and resid 220 through 247 removed outlier: 3.656A pdb=" N ILE B 238 " --> pdb=" O PHE B 234 " (cutoff:3.500A) Proline residue: B 239 - end of helix removed outlier: 3.835A pdb=" N THR B 247 " --> pdb=" O SER B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 267 removed outlier: 3.988A pdb=" N LEU B 257 " --> pdb=" O THR B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 301 Proline residue: B 284 - end of helix Processing helix chain 'B' and resid 320 through 335 Processing helix chain 'B' and resid 339 through 359 Processing helix chain 'B' and resid 366 through 371 Processing helix chain 'B' and resid 377 through 390 removed outlier: 3.796A pdb=" N ILE B 388 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU B 389 " --> pdb=" O ILE B 385 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N PHE B 390 " --> pdb=" O VAL B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 404 removed outlier: 3.907A pdb=" N PHE B 403 " --> pdb=" O LEU B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 425 Processing helix chain 'B' and resid 426 through 446 Processing helix chain 'B' and resid 447 through 456 Processing helix chain 'B' and resid 457 through 460 Processing helix chain 'B' and resid 463 through 479 Processing helix chain 'B' and resid 483 through 503 Proline residue: B 493 - end of helix Processing helix chain 'B' and resid 505 through 517 removed outlier: 3.833A pdb=" N LEU B 509 " --> pdb=" O HIS B 505 " (cutoff:3.500A) Proline residue: B 512 - end of helix Processing helix chain 'B' and resid 527 through 535 Processing helix chain 'B' and resid 540 through 566 removed outlier: 4.198A pdb=" N LEU B 550 " --> pdb=" O ARG B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 572 Processing helix chain 'B' and resid 577 through 581 556 hydrogen bonds defined for protein. 1626 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: 2.36 Time building geometry restraints manager: 2.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1208 1.30 - 1.43: 2184 1.43 - 1.55: 5264 1.55 - 1.68: 16 1.68 - 1.81: 90 Bond restraints: 8762 Sorted by residual: bond pdb=" C PRO A 83 " pdb=" O PRO A 83 " ideal model delta sigma weight residual 1.237 1.176 0.061 1.32e-02 5.74e+03 2.14e+01 bond pdb=" C PRO B 83 " pdb=" O PRO B 83 " ideal model delta sigma weight residual 1.237 1.177 0.061 1.32e-02 5.74e+03 2.12e+01 bond pdb=" C GLN A 84 " pdb=" O GLN A 84 " ideal model delta sigma weight residual 1.236 1.190 0.046 1.28e-02 6.10e+03 1.28e+01 bond pdb=" C GLN B 84 " pdb=" O GLN B 84 " ideal model delta sigma weight residual 1.236 1.191 0.045 1.28e-02 6.10e+03 1.25e+01 bond pdb=" C PHE A 86 " pdb=" O PHE A 86 " ideal model delta sigma weight residual 1.235 1.189 0.046 1.41e-02 5.03e+03 1.06e+01 ... (remaining 8757 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.38: 11373 1.38 - 2.76: 403 2.76 - 4.13: 93 4.13 - 5.51: 39 5.51 - 6.89: 12 Bond angle restraints: 11920 Sorted by residual: angle pdb=" CA LEU B 87 " pdb=" C LEU B 87 " pdb=" O LEU B 87 " ideal model delta sigma weight residual 121.87 114.98 6.89 1.10e+00 8.26e-01 3.92e+01 angle pdb=" CA LEU A 87 " pdb=" C LEU A 87 " pdb=" O LEU A 87 " ideal model delta sigma weight residual 121.87 114.99 6.88 1.10e+00 8.26e-01 3.92e+01 angle pdb=" CA LEU A 87 " pdb=" C LEU A 87 " pdb=" N ASP A 88 " ideal model delta sigma weight residual 115.30 121.99 -6.69 1.33e+00 5.65e-01 2.53e+01 angle pdb=" CA LEU B 87 " pdb=" C LEU B 87 " pdb=" N ASP B 88 " ideal model delta sigma weight residual 115.30 121.97 -6.67 1.33e+00 5.65e-01 2.51e+01 angle pdb=" O CYS A 82 " pdb=" C CYS A 82 " pdb=" N PRO A 83 " ideal model delta sigma weight residual 120.71 117.45 3.26 9.40e-01 1.13e+00 1.20e+01 ... (remaining 11915 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.85: 5350 24.85 - 49.71: 162 49.71 - 74.56: 37 74.56 - 99.41: 25 99.41 - 124.27: 8 Dihedral angle restraints: 5582 sinusoidal: 2624 harmonic: 2958 Sorted by residual: dihedral pdb=" C PHE B 86 " pdb=" N PHE B 86 " pdb=" CA PHE B 86 " pdb=" CB PHE B 86 " ideal model delta harmonic sigma weight residual -122.60 -135.99 13.39 0 2.50e+00 1.60e-01 2.87e+01 dihedral pdb=" C PHE A 86 " pdb=" N PHE A 86 " pdb=" CA PHE A 86 " pdb=" CB PHE A 86 " ideal model delta harmonic sigma weight residual -122.60 -135.98 13.38 0 2.50e+00 1.60e-01 2.86e+01 dihedral pdb=" N PHE B 86 " pdb=" C PHE B 86 " pdb=" CA PHE B 86 " pdb=" CB PHE B 86 " ideal model delta harmonic sigma weight residual 122.80 134.36 -11.56 0 2.50e+00 1.60e-01 2.14e+01 ... (remaining 5579 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 1323 0.098 - 0.195: 61 0.195 - 0.293: 2 0.293 - 0.390: 2 0.390 - 0.488: 2 Chirality restraints: 1390 Sorted by residual: chirality pdb=" CA PHE B 86 " pdb=" N PHE B 86 " pdb=" C PHE B 86 " pdb=" CB PHE B 86 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.94e+00 chirality pdb=" CA PHE A 86 " pdb=" N PHE A 86 " pdb=" C PHE A 86 " pdb=" CB PHE A 86 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.92e+00 chirality pdb=" CA LEU B 87 " pdb=" N LEU B 87 " pdb=" C LEU B 87 " pdb=" CB LEU B 87 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.41e+00 ... (remaining 1387 not shown) Planarity restraints: 1384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS B 82 " -0.011 2.00e-02 2.50e+03 2.04e-02 4.16e+00 pdb=" C CYS B 82 " 0.035 2.00e-02 2.50e+03 pdb=" O CYS B 82 " -0.012 2.00e-02 2.50e+03 pdb=" N PRO B 83 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 82 " 0.011 2.00e-02 2.50e+03 2.04e-02 4.15e+00 pdb=" C CYS A 82 " -0.035 2.00e-02 2.50e+03 pdb=" O CYS A 82 " 0.012 2.00e-02 2.50e+03 pdb=" N PRO A 83 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 527 " 0.028 5.00e-02 4.00e+02 4.24e-02 2.88e+00 pdb=" N PRO B 528 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 528 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 528 " 0.023 5.00e-02 4.00e+02 ... (remaining 1381 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 605 2.74 - 3.28: 8786 3.28 - 3.82: 15290 3.82 - 4.36: 18000 4.36 - 4.90: 31043 Nonbonded interactions: 73724 Sorted by model distance: nonbonded pdb=" O LEU B 561 " pdb=" OG1 THR B 565 " model vdw 2.198 3.040 nonbonded pdb=" O LEU A 561 " pdb=" OG1 THR A 565 " model vdw 2.198 3.040 nonbonded pdb=" OD1 ASN B 484 " pdb="NA NA B 702 " model vdw 2.289 2.470 nonbonded pdb=" OD1 ASN A 484 " pdb="NA NA A 702 " model vdw 2.290 2.470 nonbonded pdb=" NZ LYS A 10 " pdb=" O TRP B 401 " model vdw 2.293 3.120 ... (remaining 73719 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.660 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: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.840 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 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 : 0.005 0.061 8762 Z= 0.303 Angle : 0.675 6.889 11920 Z= 0.357 Chirality : 0.049 0.488 1390 Planarity : 0.006 0.057 1384 Dihedral : 15.064 124.265 3658 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 0.47 % Allowed : 0.70 % Favored : 98.84 % Cbeta Deviations : 0.21 % 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: 2.18 (0.27), residues: 1014 helix: 1.77 (0.19), residues: 784 sheet: None (None), residues: 0 loop : 0.52 (0.45), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 418 HIS 0.008 0.002 HIS A 457 PHE 0.028 0.002 PHE A 363 TYR 0.017 0.002 TYR B 85 ARG 0.003 0.001 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 142 time to evaluate : 0.820 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 144 average time/residue: 1.4493 time to fit residues: 220.9992 Evaluate side-chains 119 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 117 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain B residue 86 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 41 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 30 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 457 HIS B 538 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8762 Z= 0.204 Angle : 0.613 8.467 11920 Z= 0.296 Chirality : 0.043 0.140 1390 Planarity : 0.005 0.046 1384 Dihedral : 11.461 88.956 1836 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 0.81 % Allowed : 4.88 % Favored : 94.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.24 (0.27), residues: 1014 helix: 1.82 (0.18), residues: 790 sheet: None (None), residues: 0 loop : 0.44 (0.47), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 418 HIS 0.011 0.003 HIS B 457 PHE 0.020 0.002 PHE B 363 TYR 0.011 0.001 TYR B 226 ARG 0.004 0.001 ARG A 15 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 125 time to evaluate : 0.920 Fit side-chains revert: symmetry clash REVERT: B 510 MET cc_start: 0.8917 (mtp) cc_final: 0.8603 (mtp) outliers start: 7 outliers final: 3 residues processed: 128 average time/residue: 1.2071 time to fit residues: 165.5883 Evaluate side-chains 114 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 111 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 525 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 10.0000 chunk 28 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 92 optimal weight: 5.9990 chunk 100 optimal weight: 0.7980 chunk 82 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 457 HIS A 538 HIS B 457 HIS B 538 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8762 Z= 0.206 Angle : 0.577 7.132 11920 Z= 0.286 Chirality : 0.043 0.152 1390 Planarity : 0.005 0.046 1384 Dihedral : 10.299 88.343 1836 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 0.70 % Allowed : 7.21 % Favored : 92.09 % 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: 2.30 (0.27), residues: 1014 helix: 1.87 (0.18), residues: 790 sheet: None (None), residues: 0 loop : 0.44 (0.47), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 418 HIS 0.017 0.004 HIS A 538 PHE 0.018 0.002 PHE A 352 TYR 0.008 0.001 TYR B 226 ARG 0.005 0.000 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 116 time to evaluate : 0.878 Fit side-chains revert: symmetry clash REVERT: B 86 PHE cc_start: 0.8735 (OUTLIER) cc_final: 0.7538 (t80) REVERT: B 151 MET cc_start: 0.8535 (mmm) cc_final: 0.8064 (mmm) REVERT: B 445 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.6923 (mp0) outliers start: 6 outliers final: 2 residues processed: 119 average time/residue: 1.1220 time to fit residues: 143.7194 Evaluate side-chains 112 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 108 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain B residue 525 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 98 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 26 optimal weight: 0.0980 chunk 82 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN A 457 HIS B 457 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8762 Z= 0.173 Angle : 0.534 6.829 11920 Z= 0.265 Chirality : 0.041 0.166 1390 Planarity : 0.005 0.046 1384 Dihedral : 10.274 88.786 1836 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.51 % Allowed : 8.49 % Favored : 90.00 % 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: 2.44 (0.27), residues: 1014 helix: 2.00 (0.18), residues: 792 sheet: None (None), residues: 0 loop : 0.34 (0.47), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 418 HIS 0.017 0.003 HIS A 457 PHE 0.018 0.001 PHE A 352 TYR 0.006 0.001 TYR B 226 ARG 0.006 0.000 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 0.782 Fit side-chains revert: symmetry clash REVERT: A 86 PHE cc_start: 0.8636 (OUTLIER) cc_final: 0.7137 (t80) REVERT: A 445 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.6816 (mp0) REVERT: B 86 PHE cc_start: 0.8690 (OUTLIER) cc_final: 0.7316 (t80) outliers start: 13 outliers final: 4 residues processed: 120 average time/residue: 1.1127 time to fit residues: 143.8482 Evaluate side-chains 116 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 109 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 231 TRP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 525 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 84 optimal weight: 0.3980 chunk 68 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 50 optimal weight: 0.4980 chunk 88 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN A 457 HIS B 457 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8762 Z= 0.264 Angle : 0.607 7.461 11920 Z= 0.303 Chirality : 0.045 0.176 1390 Planarity : 0.006 0.045 1384 Dihedral : 10.691 88.714 1836 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.63 % Allowed : 8.84 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.22 (0.27), residues: 1014 helix: 1.80 (0.18), residues: 790 sheet: None (None), residues: 0 loop : 0.44 (0.47), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 418 HIS 0.020 0.003 HIS A 457 PHE 0.021 0.002 PHE A 352 TYR 0.011 0.001 TYR B 226 ARG 0.010 0.001 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 1.097 Fit side-chains revert: symmetry clash REVERT: A 413 GLU cc_start: 0.7197 (mm-30) cc_final: 0.6730 (tm-30) REVERT: B 86 PHE cc_start: 0.8772 (OUTLIER) cc_final: 0.7344 (t80) REVERT: B 151 MET cc_start: 0.8519 (mmm) cc_final: 0.8025 (mmm) REVERT: B 231 TRP cc_start: 0.8660 (OUTLIER) cc_final: 0.8031 (t-100) outliers start: 14 outliers final: 4 residues processed: 123 average time/residue: 1.0708 time to fit residues: 142.4244 Evaluate side-chains 112 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 106 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 231 TRP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 525 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 32 optimal weight: 0.0040 chunk 51 optimal weight: 6.9990 chunk 95 optimal weight: 0.0970 chunk 11 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN A 457 HIS A 538 HIS B 457 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8762 Z= 0.167 Angle : 0.535 7.394 11920 Z= 0.266 Chirality : 0.041 0.178 1390 Planarity : 0.005 0.049 1384 Dihedral : 10.378 89.880 1836 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 1.28 % Allowed : 9.88 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.40 (0.27), residues: 1014 helix: 1.96 (0.18), residues: 792 sheet: None (None), residues: 0 loop : 0.38 (0.47), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 418 HIS 0.018 0.003 HIS A 457 PHE 0.018 0.001 PHE A 352 TYR 0.005 0.001 TYR A 240 ARG 0.011 0.001 ARG B 227 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 0.945 Fit side-chains revert: symmetry clash REVERT: A 86 PHE cc_start: 0.8610 (OUTLIER) cc_final: 0.6808 (t80) REVERT: A 338 ILE cc_start: 0.7772 (OUTLIER) cc_final: 0.7282 (mt) REVERT: A 413 GLU cc_start: 0.7228 (mm-30) cc_final: 0.6772 (tm-30) REVERT: A 445 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.6855 (mp0) REVERT: B 86 PHE cc_start: 0.8688 (OUTLIER) cc_final: 0.7298 (t80) REVERT: B 151 MET cc_start: 0.8500 (mmm) cc_final: 0.8019 (mmm) REVERT: B 227 ARG cc_start: 0.7140 (mtp-110) cc_final: 0.6839 (ttp-110) REVERT: B 231 TRP cc_start: 0.8648 (OUTLIER) cc_final: 0.8014 (t-100) outliers start: 11 outliers final: 2 residues processed: 119 average time/residue: 1.0699 time to fit residues: 137.8863 Evaluate side-chains 114 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 107 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 231 TRP Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 0.0050 chunk 55 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 59 optimal weight: 0.4980 chunk 45 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 39 optimal weight: 5.9990 chunk 58 optimal weight: 0.0670 chunk 29 optimal weight: 0.7980 overall best weight: 0.4332 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN A 457 HIS A 538 HIS B 457 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8762 Z= 0.159 Angle : 0.522 6.704 11920 Z= 0.260 Chirality : 0.041 0.187 1390 Planarity : 0.005 0.051 1384 Dihedral : 10.159 89.517 1836 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 1.51 % Allowed : 10.35 % Favored : 88.14 % 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: 2.49 (0.27), residues: 1014 helix: 2.04 (0.18), residues: 792 sheet: None (None), residues: 0 loop : 0.35 (0.46), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 418 HIS 0.017 0.003 HIS A 457 PHE 0.018 0.001 PHE A 352 TYR 0.005 0.001 TYR B 332 ARG 0.012 0.001 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.905 Fit side-chains revert: symmetry clash REVERT: A 86 PHE cc_start: 0.8536 (OUTLIER) cc_final: 0.6894 (t80) REVERT: A 227 ARG cc_start: 0.7339 (mtp-110) cc_final: 0.7009 (ttp-110) REVERT: A 338 ILE cc_start: 0.7794 (OUTLIER) cc_final: 0.7304 (mt) REVERT: A 413 GLU cc_start: 0.7227 (mm-30) cc_final: 0.6788 (tm-30) REVERT: A 445 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.6854 (mp0) REVERT: B 86 PHE cc_start: 0.8653 (OUTLIER) cc_final: 0.7102 (t80) REVERT: B 231 TRP cc_start: 0.8643 (OUTLIER) cc_final: 0.8055 (t-100) REVERT: B 338 ILE cc_start: 0.7869 (OUTLIER) cc_final: 0.7431 (mt) outliers start: 13 outliers final: 3 residues processed: 123 average time/residue: 1.1244 time to fit residues: 148.7077 Evaluate side-chains 119 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 110 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 231 TRP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 338 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 chunk 85 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN A 457 HIS A 538 HIS B 457 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8762 Z= 0.182 Angle : 0.542 6.895 11920 Z= 0.270 Chirality : 0.042 0.185 1390 Planarity : 0.005 0.060 1384 Dihedral : 10.120 89.441 1836 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 1.40 % Allowed : 10.81 % Favored : 87.79 % 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: 2.42 (0.27), residues: 1014 helix: 1.98 (0.18), residues: 792 sheet: None (None), residues: 0 loop : 0.36 (0.46), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 418 HIS 0.018 0.003 HIS A 457 PHE 0.018 0.001 PHE A 352 TYR 0.007 0.001 TYR B 226 ARG 0.012 0.001 ARG B 227 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.973 Fit side-chains revert: symmetry clash REVERT: A 86 PHE cc_start: 0.8593 (OUTLIER) cc_final: 0.6868 (t80) REVERT: A 338 ILE cc_start: 0.7820 (OUTLIER) cc_final: 0.7322 (mt) REVERT: A 413 GLU cc_start: 0.7268 (mm-30) cc_final: 0.6838 (tm-30) REVERT: A 445 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.6845 (mp0) REVERT: B 86 PHE cc_start: 0.8675 (OUTLIER) cc_final: 0.7152 (t80) REVERT: B 227 ARG cc_start: 0.7132 (mtp-110) cc_final: 0.6826 (ttp-110) REVERT: B 231 TRP cc_start: 0.8627 (OUTLIER) cc_final: 0.8018 (t-100) REVERT: B 338 ILE cc_start: 0.7881 (OUTLIER) cc_final: 0.7434 (mt) outliers start: 12 outliers final: 3 residues processed: 117 average time/residue: 1.0650 time to fit residues: 134.5359 Evaluate side-chains 117 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 108 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 231 TRP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 338 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 82 optimal weight: 0.6980 chunk 86 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 96 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 67 optimal weight: 0.0170 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN A 457 HIS A 538 HIS B 457 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8762 Z= 0.177 Angle : 0.541 6.854 11920 Z= 0.269 Chirality : 0.041 0.189 1390 Planarity : 0.006 0.058 1384 Dihedral : 10.077 89.157 1836 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 1.63 % Allowed : 10.58 % Favored : 87.79 % 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: 2.40 (0.27), residues: 1014 helix: 1.98 (0.18), residues: 792 sheet: None (None), residues: 0 loop : 0.30 (0.46), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 418 HIS 0.019 0.003 HIS A 457 PHE 0.018 0.001 PHE A 352 TYR 0.005 0.001 TYR B 332 ARG 0.014 0.001 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 0.975 Fit side-chains revert: symmetry clash REVERT: A 86 PHE cc_start: 0.8568 (OUTLIER) cc_final: 0.6844 (t80) REVERT: A 227 ARG cc_start: 0.7345 (mtp-110) cc_final: 0.6982 (ttp-110) REVERT: A 338 ILE cc_start: 0.7795 (OUTLIER) cc_final: 0.7296 (mt) REVERT: A 445 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.6849 (mp0) REVERT: B 86 PHE cc_start: 0.8668 (OUTLIER) cc_final: 0.7133 (t80) REVERT: B 151 MET cc_start: 0.8491 (mmm) cc_final: 0.7957 (mmm) REVERT: B 227 ARG cc_start: 0.7071 (mtp-110) cc_final: 0.6864 (ttp-110) REVERT: B 231 TRP cc_start: 0.8629 (OUTLIER) cc_final: 0.8087 (t-100) REVERT: B 338 ILE cc_start: 0.7882 (OUTLIER) cc_final: 0.7428 (mt) outliers start: 14 outliers final: 4 residues processed: 118 average time/residue: 1.0205 time to fit residues: 130.4542 Evaluate side-chains 116 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 231 TRP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 338 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 80 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN A 457 HIS B 457 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8762 Z= 0.220 Angle : 0.577 7.186 11920 Z= 0.288 Chirality : 0.043 0.201 1390 Planarity : 0.006 0.056 1384 Dihedral : 10.316 89.900 1836 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 1.51 % Allowed : 10.93 % Favored : 87.56 % 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: 2.28 (0.27), residues: 1014 helix: 1.87 (0.18), residues: 792 sheet: None (None), residues: 0 loop : 0.34 (0.47), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 418 HIS 0.019 0.004 HIS A 457 PHE 0.019 0.002 PHE A 352 TYR 0.008 0.001 TYR B 332 ARG 0.014 0.001 ARG A 227 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.847 Fit side-chains revert: symmetry clash REVERT: A 55 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7108 (mt-10) REVERT: A 86 PHE cc_start: 0.8635 (OUTLIER) cc_final: 0.6792 (t80) REVERT: A 227 ARG cc_start: 0.7343 (mtp-110) cc_final: 0.6949 (ttp-110) REVERT: A 338 ILE cc_start: 0.7798 (OUTLIER) cc_final: 0.7387 (mt) REVERT: A 445 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.6872 (mp0) REVERT: B 86 PHE cc_start: 0.8716 (OUTLIER) cc_final: 0.7228 (t80) REVERT: B 151 MET cc_start: 0.8513 (mmm) cc_final: 0.8003 (mmm) REVERT: B 227 ARG cc_start: 0.7102 (mtp-110) cc_final: 0.6833 (ttp-110) REVERT: B 231 TRP cc_start: 0.8640 (OUTLIER) cc_final: 0.8044 (t-100) REVERT: B 338 ILE cc_start: 0.7928 (OUTLIER) cc_final: 0.7451 (mt) REVERT: B 546 ARG cc_start: 0.7836 (OUTLIER) cc_final: 0.7129 (tpt170) outliers start: 13 outliers final: 4 residues processed: 118 average time/residue: 1.0735 time to fit residues: 136.8786 Evaluate side-chains 120 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 231 TRP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain B residue 546 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN A 457 HIS B 457 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.147564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.107599 restraints weight = 7804.915| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.39 r_work: 0.3168 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8762 Z= 0.188 Angle : 0.551 6.986 11920 Z= 0.274 Chirality : 0.042 0.191 1390 Planarity : 0.005 0.054 1384 Dihedral : 10.274 89.441 1836 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 1.51 % Allowed : 10.58 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.27), residues: 1014 helix: 1.91 (0.18), residues: 792 sheet: None (None), residues: 0 loop : 0.33 (0.46), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 418 HIS 0.018 0.003 HIS A 457 PHE 0.018 0.001 PHE A 352 TYR 0.005 0.001 TYR B 332 ARG 0.013 0.001 ARG A 227 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3167.63 seconds wall clock time: 57 minutes 39.42 seconds (3459.42 seconds total)