Starting phenix.real_space_refine on Thu Sep 10 23:08:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/20zn_67436/09_2026/20zn_67436.cif Found real_map, /net/cci-nas-00/data/ceres_data/20zn_67436/09_2026/20zn_67436.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/20zn_67436/09_2026/20zn_67436.map" default_real_map = "/net/cci-nas-00/data/ceres_data/20zn_67436/09_2026/20zn_67436.map" model { file = "/net/cci-nas-00/data/ceres_data/20zn_67436/09_2026/20zn_67436.cif" } default_model = "/net/cci-nas-00/data/ceres_data/20zn_67436/09_2026/20zn_67436.cif" } resolution = 2.76 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.017 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 3 5.49 5 Mg 1 5.21 5 S 24 5.16 5 C 3179 2.51 5 N 841 2.21 5 O 892 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4940 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 608, 4868 Classifications: {'peptide': 608} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 584} Chain: "A" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 72 Unusual residues: {' MG': 1, 'ATP': 1, 'OLA': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 1.44, per 1000 atoms: 0.29 Number of scatterers: 4940 At special positions: 0 Unit cell: (77.52, 92.34, 86.07, 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 24 16.00 P 3 15.00 Mg 1 11.99 O 892 8.00 N 841 7.00 C 3179 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: 0.47 Conformation dependent library (CDL) restraints added in 182.5 milliseconds 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1130 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 7 sheets defined 39.0% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 14 through 23 Processing helix chain 'A' and resid 25 through 49 removed outlier: 3.625A pdb=" N ARG A 49 " --> pdb=" O SER A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 66 removed outlier: 3.560A pdb=" N ALA A 58 " --> pdb=" O THR A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 98 Processing helix chain 'A' and resid 114 through 128 removed outlier: 3.857A pdb=" N VAL A 118 " --> pdb=" O GLU A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 151 removed outlier: 3.648A pdb=" N CYS A 150 " --> pdb=" O CYS A 146 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLY A 151 " --> pdb=" O PHE A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 167 Processing helix chain 'A' and resid 168 through 174 Processing helix chain 'A' and resid 194 through 199 Processing helix chain 'A' and resid 207 through 212 removed outlier: 3.703A pdb=" N SER A 212 " --> pdb=" O SER A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 253 removed outlier: 3.967A pdb=" N LEU A 248 " --> pdb=" O TYR A 244 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N THR A 249 " --> pdb=" O GLY A 245 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY A 253 " --> pdb=" O THR A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 273 Processing helix chain 'A' and resid 274 through 283 Processing helix chain 'A' and resid 296 through 304 Processing helix chain 'A' and resid 314 through 321 Processing helix chain 'A' and resid 342 through 354 Processing helix chain 'A' and resid 385 through 390 Processing helix chain 'A' and resid 441 through 448 Processing helix chain 'A' and resid 493 through 503 removed outlier: 3.655A pdb=" N VAL A 497 " --> pdb=" O ALA A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 550 Processing helix chain 'A' and resid 575 through 582 Processing helix chain 'A' and resid 606 through 615 Processing sheet with id=AA1, first strand: chain 'A' and resid 78 through 80 removed outlier: 6.903A pdb=" N LEU A 79 " --> pdb=" O PHE A 71 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN A 339 " --> pdb=" O TYR A 311 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ALA A 336 " --> pdb=" O TYR A 359 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N PHE A 361 " --> pdb=" O ALA A 336 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLY A 338 " --> pdb=" O PHE A 361 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N ALA A 363 " --> pdb=" O GLY A 338 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 192 through 193 removed outlier: 6.174A pdb=" N LEU A 155 " --> pdb=" O TYR A 180 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N VAL A 154 " --> pdb=" O CYS A 106 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL A 107 " --> pdb=" O ALA A 132 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N MET A 131 " --> pdb=" O TYR A 222 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N TYR A 224 " --> pdb=" O MET A 131 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N CYS A 133 " --> pdb=" O TYR A 224 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 382 through 383 removed outlier: 6.852A pdb=" N LEU A 466 " --> pdb=" O HIS A 478 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ARG A 480 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N GLY A 464 " --> pdb=" O ARG A 480 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N LEU A 425 " --> pdb=" O SER A 463 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ASP A 465 " --> pdb=" O GLY A 423 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLY A 423 " --> pdb=" O ASP A 465 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 382 through 383 removed outlier: 6.852A pdb=" N LEU A 466 " --> pdb=" O HIS A 478 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ARG A 480 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N GLY A 464 " --> pdb=" O ARG A 480 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 399 through 400 Processing sheet with id=AA6, first strand: chain 'A' and resid 485 through 487 Processing sheet with id=AA7, first strand: chain 'A' and resid 507 through 515 removed outlier: 7.024A pdb=" N GLY A 525 " --> pdb=" O PHE A 558 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N ARG A 560 " --> pdb=" O GLY A 525 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ALA A 527 " --> pdb=" O ARG A 560 " (cutoff:3.500A) 205 hydrogen bonds defined for protein. 579 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: 0.89 Time building geometry restraints manager: 0.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1577 1.34 - 1.46: 1049 1.46 - 1.58: 2388 1.58 - 1.69: 5 1.69 - 1.81: 34 Bond restraints: 5053 Sorted by residual: bond pdb=" C4 ATP A 701 " pdb=" C5 ATP A 701 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.21e+01 bond pdb=" C5 ATP A 701 " pdb=" C6 ATP A 701 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.33e+01 bond pdb=" C5 ATP A 701 " pdb=" N7 ATP A 701 " ideal model delta sigma weight residual 1.387 1.341 0.046 1.00e-02 1.00e+04 2.11e+01 bond pdb=" C4 ATP A 701 " pdb=" N9 ATP A 701 " ideal model delta sigma weight residual 1.374 1.330 0.044 1.00e-02 1.00e+04 1.93e+01 bond pdb=" C8 ATP A 701 " pdb=" N7 ATP A 701 " ideal model delta sigma weight residual 1.310 1.351 -0.041 1.00e-02 1.00e+04 1.68e+01 ... (remaining 5048 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.57: 6796 3.57 - 7.13: 33 7.13 - 10.70: 7 10.70 - 14.26: 0 14.26 - 17.83: 2 Bond angle restraints: 6838 Sorted by residual: angle pdb=" PB ATP A 701 " pdb=" O3B ATP A 701 " pdb=" PG ATP A 701 " ideal model delta sigma weight residual 139.87 122.04 17.83 1.00e+00 1.00e+00 3.18e+02 angle pdb=" PA ATP A 701 " pdb=" O3A ATP A 701 " pdb=" PB ATP A 701 " ideal model delta sigma weight residual 136.83 122.56 14.27 1.00e+00 1.00e+00 2.04e+02 angle pdb=" C5 ATP A 701 " pdb=" C4 ATP A 701 " pdb=" N3 ATP A 701 " ideal model delta sigma weight residual 126.80 119.01 7.79 1.00e+00 1.00e+00 6.07e+01 angle pdb=" N3 ATP A 701 " pdb=" C4 ATP A 701 " pdb=" N9 ATP A 701 " ideal model delta sigma weight residual 127.04 135.07 -8.03 1.15e+00 7.59e-01 4.89e+01 angle pdb=" N1 ATP A 701 " pdb=" C2 ATP A 701 " pdb=" N3 ATP A 701 " ideal model delta sigma weight residual 128.69 123.64 5.05 1.00e+00 1.00e+00 2.55e+01 ... (remaining 6833 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.84: 2708 16.84 - 33.67: 228 33.67 - 50.51: 64 50.51 - 67.35: 19 67.35 - 84.19: 5 Dihedral angle restraints: 3024 sinusoidal: 1255 harmonic: 1769 Sorted by residual: dihedral pdb=" CA ARG A 139 " pdb=" C ARG A 139 " pdb=" N ALA A 140 " pdb=" CA ALA A 140 " ideal model delta harmonic sigma weight residual -180.00 -152.17 -27.83 0 5.00e+00 4.00e-02 3.10e+01 dihedral pdb=" C GLN A 562 " pdb=" N GLN A 562 " pdb=" CA GLN A 562 " pdb=" CB GLN A 562 " ideal model delta harmonic sigma weight residual -122.60 -112.88 -9.72 0 2.50e+00 1.60e-01 1.51e+01 dihedral pdb=" CA ASP A 395 " pdb=" C ASP A 395 " pdb=" N LEU A 396 " pdb=" CA LEU A 396 " ideal model delta harmonic sigma weight residual 180.00 162.02 17.98 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 3021 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 644 0.066 - 0.133: 96 0.133 - 0.199: 5 0.199 - 0.266: 2 0.266 - 0.332: 2 Chirality restraints: 749 Sorted by residual: chirality pdb=" CA ARG A 480 " pdb=" N ARG A 480 " pdb=" C ARG A 480 " pdb=" CB ARG A 480 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" CA GLN A 562 " pdb=" N GLN A 562 " pdb=" C GLN A 562 " pdb=" CB GLN A 562 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" CA LEU A 618 " pdb=" N LEU A 618 " pdb=" C LEU A 618 " pdb=" CB LEU A 618 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 746 not shown) Planarity restraints: 866 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 119 " 0.015 2.00e-02 2.50e+03 1.02e-02 2.60e+00 pdb=" CG TRP A 119 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP A 119 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TRP A 119 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 119 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 119 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 119 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 119 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 119 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 119 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 119 " -0.007 2.00e-02 2.50e+03 1.38e-02 1.90e+00 pdb=" C TRP A 119 " 0.024 2.00e-02 2.50e+03 pdb=" O TRP A 119 " -0.009 2.00e-02 2.50e+03 pdb=" N LEU A 120 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 15 " 0.021 5.00e-02 4.00e+02 3.20e-02 1.64e+00 pdb=" N PRO A 16 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 16 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 16 " 0.018 5.00e-02 4.00e+02 ... (remaining 863 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 1510 2.82 - 3.34: 4272 3.34 - 3.86: 8711 3.86 - 4.38: 10427 4.38 - 4.90: 17515 Nonbonded interactions: 42435 Sorted by model distance: nonbonded pdb=" O1B ATP A 701 " pdb="MG MG A 702 " model vdw 2.305 2.170 nonbonded pdb=" OH TYR A 399 " pdb=" OD1 ASP A 404 " model vdw 2.328 3.040 nonbonded pdb=" OE2 GLU A 366 " pdb=" OH TYR A 438 " model vdw 2.342 3.040 nonbonded pdb=" O CYS A 320 " pdb=" NH1 ARG A 352 " model vdw 2.358 3.120 nonbonded pdb=" O CYS A 146 " pdb=" OH TYR A 224 " model vdw 2.359 3.040 ... (remaining 42430 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 5.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.490 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:10.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 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 0.079 5053 Z= 0.340 Angle : 0.822 17.828 6838 Z= 0.562 Chirality : 0.050 0.332 749 Planarity : 0.004 0.032 866 Dihedral : 14.735 84.186 1894 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.12 % Allowed : 9.23 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.30), residues: 606 helix: -1.42 (0.30), residues: 226 sheet: -1.46 (0.55), residues: 79 loop : -0.93 (0.31), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 289 TYR 0.013 0.001 TYR A 362 PHE 0.010 0.001 PHE A 349 TRP 0.028 0.003 TRP A 119 HIS 0.004 0.001 HIS A 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.34 ( 5053) covalent geometry : angle 0.82222 / 0.56 ( 6838) hydrogen bonds : bond 0.14650 / 9.63 ( 200) hydrogen bonds : angle 7.61573 / 5.66 ( 579) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.210 Fit side-chains REVERT: A 41 ARG cc_start: 0.7243 (mtm-85) cc_final: 0.6934 (ttp-110) REVERT: A 255 LYS cc_start: 0.8072 (mmtt) cc_final: 0.7682 (mtmt) REVERT: A 395 ASP cc_start: 0.8293 (m-30) cc_final: 0.8073 (m-30) REVERT: A 446 GLU cc_start: 0.7307 (mm-30) cc_final: 0.7023 (tm-30) REVERT: A 549 TYR cc_start: 0.7380 (m-80) cc_final: 0.6429 (m-80) outliers start: 11 outliers final: 5 residues processed: 87 average time/residue: 0.7652 time to fit residues: 68.5415 Evaluate side-chains 61 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 430 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 26 optimal weight: 0.0970 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 GLN A 491 ASN A 535 HIS A 544 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.145679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.120130 restraints weight = 5795.034| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.72 r_work: 0.3243 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5053 Z= 0.125 Angle : 0.481 6.854 6838 Z= 0.259 Chirality : 0.042 0.175 749 Planarity : 0.004 0.033 866 Dihedral : 9.983 73.600 747 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.31 % Allowed : 12.31 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.33), residues: 606 helix: -0.01 (0.34), residues: 232 sheet: -1.17 (0.56), residues: 78 loop : -0.36 (0.34), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 57 TYR 0.012 0.001 TYR A 136 PHE 0.010 0.001 PHE A 485 TRP 0.024 0.002 TRP A 119 HIS 0.003 0.001 HIS A 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.12 ( 5053) covalent geometry : angle 0.48094 / 0.26 ( 6838) hydrogen bonds : bond 0.03866 / 2.51 ( 200) hydrogen bonds : angle 5.59605 / 4.16 ( 579) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.221 Fit side-chains REVERT: A 255 LYS cc_start: 0.8352 (mmtt) cc_final: 0.7727 (mtmt) outliers start: 12 outliers final: 4 residues processed: 62 average time/residue: 0.6029 time to fit residues: 38.8988 Evaluate side-chains 51 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 398 LYS Chi-restraints excluded: chain A residue 603 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 31 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 3 optimal weight: 0.3980 chunk 22 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 10 optimal weight: 0.0980 chunk 5 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 478 HIS A 562 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.145834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.120170 restraints weight = 5737.661| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.72 r_work: 0.3242 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 5053 Z= 0.114 Angle : 0.462 6.758 6838 Z= 0.247 Chirality : 0.042 0.176 749 Planarity : 0.003 0.029 866 Dihedral : 9.179 67.370 741 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.50 % Allowed : 13.27 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.33), residues: 606 helix: 0.33 (0.34), residues: 232 sheet: -0.89 (0.56), residues: 78 loop : -0.14 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 57 TYR 0.012 0.001 TYR A 136 PHE 0.010 0.001 PHE A 485 TRP 0.026 0.002 TRP A 119 HIS 0.002 0.001 HIS A 478 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.11 ( 5053) covalent geometry : angle 0.46153 / 0.25 ( 6838) hydrogen bonds : bond 0.03624 / 2.33 ( 200) hydrogen bonds : angle 5.24387 / 3.87 ( 579) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.249 Fit side-chains revert: symmetry clash REVERT: A 185 THR cc_start: 0.9118 (p) cc_final: 0.8849 (p) REVERT: A 255 LYS cc_start: 0.8359 (mmtt) cc_final: 0.7723 (mtpt) outliers start: 13 outliers final: 4 residues processed: 59 average time/residue: 0.5961 time to fit residues: 36.6730 Evaluate side-chains 52 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 398 LYS Chi-restraints excluded: chain A residue 580 GLU Chi-restraints excluded: chain A residue 603 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 52 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 39 optimal weight: 0.0980 chunk 14 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.146064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.120437 restraints weight = 5754.522| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.73 r_work: 0.3240 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5053 Z= 0.111 Angle : 0.455 6.781 6838 Z= 0.242 Chirality : 0.042 0.176 749 Planarity : 0.003 0.028 866 Dihedral : 8.959 76.613 741 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.31 % Allowed : 13.08 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.33), residues: 606 helix: 0.55 (0.34), residues: 233 sheet: -0.73 (0.57), residues: 78 loop : 0.01 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 486 TYR 0.012 0.001 TYR A 136 PHE 0.010 0.001 PHE A 485 TRP 0.026 0.002 TRP A 119 HIS 0.003 0.001 HIS A 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 ( 5053) covalent geometry : angle 0.45483 / 0.24 ( 6838) hydrogen bonds : bond 0.03429 / 2.21 ( 200) hydrogen bonds : angle 5.06745 / 3.74 ( 579) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.147 Fit side-chains revert: symmetry clash REVERT: A 41 ARG cc_start: 0.7458 (mtm-85) cc_final: 0.6914 (ttp-110) REVERT: A 185 THR cc_start: 0.9172 (OUTLIER) cc_final: 0.8914 (p) REVERT: A 192 ASP cc_start: 0.8834 (OUTLIER) cc_final: 0.8565 (t70) REVERT: A 255 LYS cc_start: 0.8375 (mmtt) cc_final: 0.7727 (mtpt) REVERT: A 324 GLN cc_start: 0.7565 (tt0) cc_final: 0.7152 (mt0) REVERT: A 372 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.7795 (tpt) REVERT: A 478 HIS cc_start: 0.7999 (OUTLIER) cc_final: 0.7596 (t70) outliers start: 12 outliers final: 4 residues processed: 61 average time/residue: 0.5353 time to fit residues: 34.0471 Evaluate side-chains 61 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 398 LYS Chi-restraints excluded: chain A residue 478 HIS Chi-restraints excluded: chain A residue 580 GLU Chi-restraints excluded: chain A residue 603 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 58 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 562 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.149295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.123432 restraints weight = 5788.779| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.75 r_work: 0.3298 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5053 Z= 0.117 Angle : 0.461 6.805 6838 Z= 0.245 Chirality : 0.042 0.178 749 Planarity : 0.003 0.028 866 Dihedral : 8.949 78.437 741 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.69 % Allowed : 12.69 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.33), residues: 606 helix: 0.66 (0.34), residues: 233 sheet: -0.78 (0.58), residues: 75 loop : 0.05 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 57 TYR 0.013 0.001 TYR A 136 PHE 0.010 0.001 PHE A 485 TRP 0.027 0.002 TRP A 119 HIS 0.003 0.001 HIS A 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 5053) covalent geometry : angle 0.46074 / 0.24 ( 6838) hydrogen bonds : bond 0.03400 / 2.20 ( 200) hydrogen bonds : angle 5.05133 / 3.73 ( 579) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.132 Fit side-chains revert: symmetry clash REVERT: A 41 ARG cc_start: 0.7451 (mtm-85) cc_final: 0.6921 (ttp-110) REVERT: A 185 THR cc_start: 0.9192 (OUTLIER) cc_final: 0.8934 (p) REVERT: A 192 ASP cc_start: 0.8841 (OUTLIER) cc_final: 0.8589 (t70) REVERT: A 255 LYS cc_start: 0.8345 (mmtt) cc_final: 0.7708 (mtpt) REVERT: A 324 GLN cc_start: 0.7614 (tt0) cc_final: 0.7199 (mt0) REVERT: A 372 MET cc_start: 0.8688 (OUTLIER) cc_final: 0.7869 (tpt) REVERT: A 478 HIS cc_start: 0.8019 (OUTLIER) cc_final: 0.7622 (t70) REVERT: A 549 TYR cc_start: 0.7493 (m-80) cc_final: 0.6427 (m-80) outliers start: 14 outliers final: 7 residues processed: 60 average time/residue: 0.5227 time to fit residues: 32.7244 Evaluate side-chains 61 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 398 LYS Chi-restraints excluded: chain A residue 478 HIS Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 580 GLU Chi-restraints excluded: chain A residue 603 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 30 optimal weight: 0.0980 chunk 15 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 562 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.147941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.121585 restraints weight = 5877.979| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.78 r_work: 0.3280 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 5053 Z= 0.139 Angle : 0.485 6.938 6838 Z= 0.255 Chirality : 0.043 0.183 749 Planarity : 0.003 0.030 866 Dihedral : 9.169 76.846 741 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.88 % Allowed : 12.12 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.33), residues: 606 helix: 0.67 (0.34), residues: 233 sheet: -0.77 (0.59), residues: 75 loop : 0.06 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 57 TYR 0.014 0.001 TYR A 136 PHE 0.010 0.001 PHE A 485 TRP 0.028 0.002 TRP A 119 HIS 0.003 0.001 HIS A 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 ( 5053) covalent geometry : angle 0.48450 / 0.25 ( 6838) hydrogen bonds : bond 0.03621 / 2.36 ( 200) hydrogen bonds : angle 5.12631 / 3.79 ( 579) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 52 time to evaluate : 0.213 Fit side-chains revert: symmetry clash REVERT: A 41 ARG cc_start: 0.7466 (mtm-85) cc_final: 0.6938 (ttp-110) REVERT: A 185 THR cc_start: 0.9205 (OUTLIER) cc_final: 0.8951 (p) REVERT: A 192 ASP cc_start: 0.8866 (OUTLIER) cc_final: 0.8618 (t70) REVERT: A 255 LYS cc_start: 0.8321 (mmtt) cc_final: 0.7687 (mtpt) REVERT: A 324 GLN cc_start: 0.7644 (tt0) cc_final: 0.7210 (mt0) REVERT: A 372 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.7874 (tpt) REVERT: A 549 TYR cc_start: 0.7517 (m-80) cc_final: 0.6553 (m-80) outliers start: 15 outliers final: 8 residues processed: 60 average time/residue: 0.6198 time to fit residues: 38.7515 Evaluate side-chains 60 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 398 LYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 580 GLU Chi-restraints excluded: chain A residue 603 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 19 optimal weight: 0.9980 chunk 5 optimal weight: 0.3980 chunk 37 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 4 optimal weight: 0.2980 chunk 53 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 55 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 GLN A 562 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.149423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.123623 restraints weight = 5769.772| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.77 r_work: 0.3302 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5053 Z= 0.111 Angle : 0.464 6.745 6838 Z= 0.244 Chirality : 0.042 0.176 749 Planarity : 0.003 0.032 866 Dihedral : 8.909 80.661 741 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.88 % Allowed : 12.12 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.33), residues: 606 helix: 0.78 (0.34), residues: 233 sheet: -0.68 (0.59), residues: 75 loop : 0.13 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 57 TYR 0.022 0.001 TYR A 394 PHE 0.009 0.001 PHE A 485 TRP 0.026 0.002 TRP A 119 HIS 0.003 0.001 HIS A 478 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 ( 5053) covalent geometry : angle 0.46376 / 0.24 ( 6838) hydrogen bonds : bond 0.03294 / 2.15 ( 200) hydrogen bonds : angle 5.00576 / 3.69 ( 579) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 53 time to evaluate : 0.199 Fit side-chains revert: symmetry clash REVERT: A 41 ARG cc_start: 0.7430 (mtm-85) cc_final: 0.6898 (ttp-110) REVERT: A 50 ARG cc_start: 0.7264 (mmp-170) cc_final: 0.6921 (mmp-170) REVERT: A 185 THR cc_start: 0.9205 (OUTLIER) cc_final: 0.8957 (p) REVERT: A 192 ASP cc_start: 0.8831 (OUTLIER) cc_final: 0.8580 (t70) REVERT: A 255 LYS cc_start: 0.8310 (mmtt) cc_final: 0.7666 (mtpt) REVERT: A 324 GLN cc_start: 0.7625 (tt0) cc_final: 0.7183 (mt0) REVERT: A 372 MET cc_start: 0.8675 (OUTLIER) cc_final: 0.7867 (tpt) REVERT: A 549 TYR cc_start: 0.7492 (m-80) cc_final: 0.6632 (m-80) outliers start: 15 outliers final: 6 residues processed: 61 average time/residue: 0.5611 time to fit residues: 35.7443 Evaluate side-chains 58 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 478 HIS Chi-restraints excluded: chain A residue 580 GLU Chi-restraints excluded: chain A residue 603 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 58 optimal weight: 4.9990 chunk 10 optimal weight: 0.0980 chunk 46 optimal weight: 0.5980 chunk 14 optimal weight: 0.0020 chunk 56 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.147197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.121743 restraints weight = 5796.698| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.73 r_work: 0.3238 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 5053 Z= 0.099 Angle : 0.453 6.624 6838 Z= 0.240 Chirality : 0.041 0.172 749 Planarity : 0.003 0.034 866 Dihedral : 8.519 85.590 741 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.92 % Allowed : 13.46 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.34), residues: 606 helix: 0.88 (0.34), residues: 233 sheet: -0.79 (0.56), residues: 86 loop : 0.23 (0.35), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 486 TYR 0.026 0.001 TYR A 394 PHE 0.008 0.001 PHE A 485 TRP 0.025 0.002 TRP A 119 HIS 0.002 0.001 HIS A 478 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 ( 5053) covalent geometry : angle 0.45347 / 0.24 ( 6838) hydrogen bonds : bond 0.03088 / 2.01 ( 200) hydrogen bonds : angle 4.89331 / 3.61 ( 579) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.195 Fit side-chains REVERT: A 41 ARG cc_start: 0.7454 (mtm-85) cc_final: 0.6910 (ttp-110) REVERT: A 185 THR cc_start: 0.9208 (OUTLIER) cc_final: 0.8958 (p) REVERT: A 192 ASP cc_start: 0.8788 (OUTLIER) cc_final: 0.8527 (t70) REVERT: A 255 LYS cc_start: 0.8323 (mmtt) cc_final: 0.7700 (mtpt) REVERT: A 324 GLN cc_start: 0.7570 (tt0) cc_final: 0.7142 (mt0) REVERT: A 351 LYS cc_start: 0.8148 (ttpp) cc_final: 0.7942 (tttm) REVERT: A 372 MET cc_start: 0.8594 (OUTLIER) cc_final: 0.7756 (tpt) REVERT: A 549 TYR cc_start: 0.7433 (m-80) cc_final: 0.6626 (m-80) outliers start: 10 outliers final: 5 residues processed: 57 average time/residue: 0.5559 time to fit residues: 33.2595 Evaluate side-chains 61 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 478 HIS Chi-restraints excluded: chain A residue 603 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 29 optimal weight: 0.0270 chunk 2 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 overall best weight: 1.5242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.142989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.117144 restraints weight = 5746.576| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 1.71 r_work: 0.3175 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 5053 Z= 0.208 Angle : 0.551 7.122 6838 Z= 0.286 Chirality : 0.045 0.189 749 Planarity : 0.004 0.035 866 Dihedral : 9.512 71.096 741 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.73 % Allowed : 13.85 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.33), residues: 606 helix: 0.65 (0.34), residues: 232 sheet: -0.72 (0.60), residues: 75 loop : 0.06 (0.34), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 480 TYR 0.023 0.002 TYR A 394 PHE 0.012 0.002 PHE A 485 TRP 0.033 0.003 TRP A 119 HIS 0.004 0.001 HIS A 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.21 ( 5053) covalent geometry : angle 0.55087 / 0.29 ( 6838) hydrogen bonds : bond 0.04195 / 2.76 ( 200) hydrogen bonds : angle 5.31018 / 3.92 ( 579) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.190 Fit side-chains REVERT: A 41 ARG cc_start: 0.7496 (mtm-85) cc_final: 0.6975 (ttp-110) REVERT: A 50 ARG cc_start: 0.7286 (mmp-170) cc_final: 0.7010 (mmp-170) REVERT: A 185 THR cc_start: 0.9216 (OUTLIER) cc_final: 0.8948 (p) REVERT: A 192 ASP cc_start: 0.8866 (OUTLIER) cc_final: 0.8591 (t70) REVERT: A 255 LYS cc_start: 0.8333 (mmtt) cc_final: 0.7686 (mtpt) REVERT: A 324 GLN cc_start: 0.7646 (tt0) cc_final: 0.7193 (mt0) REVERT: A 372 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.7851 (tpt) REVERT: A 409 ASP cc_start: 0.7043 (p0) cc_final: 0.6826 (p0) REVERT: A 549 TYR cc_start: 0.7527 (m-80) cc_final: 0.6726 (m-80) outliers start: 9 outliers final: 4 residues processed: 55 average time/residue: 0.5370 time to fit residues: 30.8775 Evaluate side-chains 56 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 478 HIS Chi-restraints excluded: chain A residue 603 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 8 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 19 optimal weight: 0.0270 chunk 35 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.146445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.121040 restraints weight = 5729.223| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.71 r_work: 0.3229 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 5053 Z= 0.105 Angle : 0.469 6.729 6838 Z= 0.248 Chirality : 0.042 0.178 749 Planarity : 0.003 0.034 866 Dihedral : 8.735 77.932 741 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.54 % Allowed : 14.04 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.33), residues: 606 helix: 0.84 (0.35), residues: 232 sheet: -0.77 (0.56), residues: 86 loop : 0.16 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 486 TYR 0.030 0.001 TYR A 394 PHE 0.009 0.001 PHE A 485 TRP 0.024 0.002 TRP A 119 HIS 0.003 0.001 HIS A 478 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.10 ( 5053) covalent geometry : angle 0.46912 / 0.25 ( 6838) hydrogen bonds : bond 0.03212 / 2.10 ( 200) hydrogen bonds : angle 4.98751 / 3.68 ( 579) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.142 Fit side-chains REVERT: A 41 ARG cc_start: 0.7468 (mtm-85) cc_final: 0.6926 (ttp-110) REVERT: A 185 THR cc_start: 0.9219 (p) cc_final: 0.8966 (p) REVERT: A 192 ASP cc_start: 0.8812 (OUTLIER) cc_final: 0.8540 (t70) REVERT: A 255 LYS cc_start: 0.8309 (mmtt) cc_final: 0.7691 (mtpt) REVERT: A 324 GLN cc_start: 0.7603 (tt0) cc_final: 0.7144 (mt0) REVERT: A 372 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.7794 (tpt) REVERT: A 409 ASP cc_start: 0.6984 (p0) cc_final: 0.6774 (p0) REVERT: A 549 TYR cc_start: 0.7467 (m-80) cc_final: 0.6725 (m-80) outliers start: 8 outliers final: 4 residues processed: 55 average time/residue: 0.5352 time to fit residues: 30.6770 Evaluate side-chains 56 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 478 HIS Chi-restraints excluded: chain A residue 603 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 17 optimal weight: 4.9990 chunk 31 optimal weight: 0.0670 chunk 42 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 24 optimal weight: 0.2980 chunk 39 optimal weight: 0.0010 overall best weight: 0.3324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.148192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.122581 restraints weight = 5798.384| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.76 r_work: 0.3290 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 5053 Z= 0.093 Angle : 0.455 6.589 6838 Z= 0.241 Chirality : 0.041 0.172 749 Planarity : 0.003 0.035 866 Dihedral : 8.073 86.518 741 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.54 % Allowed : 13.85 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.34), residues: 606 helix: 0.95 (0.35), residues: 233 sheet: -0.67 (0.56), residues: 86 loop : 0.24 (0.35), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 486 TYR 0.030 0.001 TYR A 394 PHE 0.009 0.001 PHE A 26 TRP 0.023 0.002 TRP A 119 HIS 0.002 0.001 HIS A 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.09 ( 5053) covalent geometry : angle 0.45504 / 0.24 ( 6838) hydrogen bonds : bond 0.02918 / 1.89 ( 200) hydrogen bonds : angle 4.77865 / 3.51 ( 579) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1913.92 seconds wall clock time: 33 minutes 44.37 seconds (2024.37 seconds total)