Starting phenix.real_space_refine on Mon Feb 10 22:03:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7r7n_24299/02_2025/7r7n_24299.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r7n_24299/02_2025/7r7n_24299.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7r7n_24299/02_2025/7r7n_24299.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r7n_24299/02_2025/7r7n_24299.map" model { file = "/net/cci-nas-00/data/ceres_data/7r7n_24299/02_2025/7r7n_24299.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r7n_24299/02_2025/7r7n_24299.cif" } resolution = 3.95 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.018 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: 4 Type Number sf(0) Gaussians S 17 5.16 5 C 1795 2.51 5 N 481 2.21 5 O 497 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 2790 Number of models: 1 Model: "" Number of chains: 4 Chain: "H" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 735 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain breaks: 3 Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 42 Chain: "E" Number of atoms: 1382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1382 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 10, 'TRANS': 178} Chain breaks: 1 Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 61 Chain: "L" Number of atoms: 635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 635 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 87} Chain breaks: 2 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 5, 'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 37 Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.28, per 1000 atoms: 1.18 Number of scatterers: 2790 At special positions: 0 Unit cell: (77.7, 66.15, 76.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 17 16.00 O 497 8.00 N 481 7.00 C 1795 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 103 " - pdb=" SG CYS H 108 " distance=2.12 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.09 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.21 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 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " BETA1-6 " NAG A 1 " - " FUC A 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 1 " - " ASN E 343 " Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 334.0 milliseconds 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 714 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 10 sheets defined 12.3% alpha, 38.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.808A pdb=" N TRP E 353 " --> pdb=" O VAL E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 370 Processing helix chain 'E' and resid 405 through 410 removed outlier: 4.413A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'E' and resid 438 through 443 Processing helix chain 'E' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 58 through 60 removed outlier: 5.667A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 58 through 60 removed outlier: 5.667A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.537A pdb=" N VAL E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 361 through 362 removed outlier: 6.320A pdb=" N CYS E 361 " --> pdb=" O CYS E 525 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA7, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AA8, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.603A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.564A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.564A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) 128 hydrogen bonds defined for protein. 297 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: 0.79 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 808 1.33 - 1.46: 747 1.46 - 1.58: 1283 1.58 - 1.71: 0 1.71 - 1.83: 20 Bond restraints: 2858 Sorted by residual: bond pdb=" NE ARG L 18 " pdb=" CZ ARG L 18 " ideal model delta sigma weight residual 1.326 1.367 -0.041 1.10e-02 8.26e+03 1.40e+01 bond pdb=" C5 NAG A 2 " pdb=" O5 NAG A 2 " ideal model delta sigma weight residual 1.413 1.470 -0.057 2.00e-02 2.50e+03 8.07e+00 bond pdb=" CB ILE L 2 " pdb=" CG1 ILE L 2 " ideal model delta sigma weight residual 1.530 1.582 -0.052 2.00e-02 2.50e+03 6.86e+00 bond pdb=" CB LEU E 517 " pdb=" CG LEU E 517 " ideal model delta sigma weight residual 1.530 1.579 -0.049 2.00e-02 2.50e+03 5.94e+00 bond pdb=" C5 FUC A 3 " pdb=" O5 FUC A 3 " ideal model delta sigma weight residual 1.423 1.471 -0.048 2.00e-02 2.50e+03 5.81e+00 ... (remaining 2853 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 3270 1.51 - 3.02: 527 3.02 - 4.53: 68 4.53 - 6.04: 28 6.04 - 7.54: 14 Bond angle restraints: 3907 Sorted by residual: angle pdb=" C GLY H 27 " pdb=" N PRO H 28 " pdb=" CA PRO H 28 " ideal model delta sigma weight residual 119.85 127.39 -7.54 1.01e+00 9.80e-01 5.58e+01 angle pdb=" C SER E 383 " pdb=" N PRO E 384 " pdb=" CA PRO E 384 " ideal model delta sigma weight residual 119.56 126.71 -7.15 1.02e+00 9.61e-01 4.91e+01 angle pdb=" C GLN E 498 " pdb=" N PRO E 499 " pdb=" CA PRO E 499 " ideal model delta sigma weight residual 119.87 126.95 -7.08 1.04e+00 9.25e-01 4.63e+01 angle pdb=" C ALA L 43 " pdb=" N PRO L 44 " pdb=" CA PRO L 44 " ideal model delta sigma weight residual 119.85 126.57 -6.72 1.01e+00 9.80e-01 4.42e+01 angle pdb=" C PHE E 490 " pdb=" N PRO E 491 " pdb=" CA PRO E 491 " ideal model delta sigma weight residual 119.87 126.77 -6.90 1.04e+00 9.25e-01 4.40e+01 ... (remaining 3902 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.05: 1577 13.05 - 26.10: 77 26.10 - 39.14: 14 39.14 - 52.19: 9 52.19 - 65.24: 6 Dihedral angle restraints: 1683 sinusoidal: 561 harmonic: 1122 Sorted by residual: dihedral pdb=" CB CYS H 103 " pdb=" SG CYS H 103 " pdb=" SG CYS H 108 " pdb=" CB CYS H 108 " ideal model delta sinusoidal sigma weight residual -86.00 -151.24 65.24 1 1.00e+01 1.00e-02 5.58e+01 dihedral pdb=" CB CYS E 391 " pdb=" SG CYS E 391 " pdb=" SG CYS E 525 " pdb=" CB CYS E 525 " ideal model delta sinusoidal sigma weight residual 93.00 45.49 47.51 1 1.00e+01 1.00e-02 3.12e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 62.52 30.48 1 1.00e+01 1.00e-02 1.33e+01 ... (remaining 1680 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.057: 306 0.057 - 0.114: 93 0.114 - 0.171: 26 0.171 - 0.228: 9 0.228 - 0.285: 6 Chirality restraints: 440 Sorted by residual: chirality pdb=" C1 NAG A 2 " pdb=" O4 NAG A 1 " pdb=" C2 NAG A 2 " pdb=" O5 NAG A 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.53 0.13 2.00e-02 2.50e+03 4.12e+01 chirality pdb=" C1 FUC A 3 " pdb=" O6 NAG A 1 " pdb=" C2 FUC A 3 " pdb=" O5 FUC A 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.44 0.04 2.00e-02 2.50e+03 4.68e+00 chirality pdb=" C2 NAG A 2 " pdb=" C1 NAG A 2 " pdb=" C3 NAG A 2 " pdb=" N2 NAG A 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.78 0.29 2.00e-01 2.50e+01 2.03e+00 ... (remaining 437 not shown) Planarity restraints: 505 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR E 489 " 0.008 2.00e-02 2.50e+03 1.63e-02 2.66e+00 pdb=" C TYR E 489 " -0.028 2.00e-02 2.50e+03 pdb=" O TYR E 489 " 0.011 2.00e-02 2.50e+03 pdb=" N PHE E 490 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 92 " -0.021 2.00e-02 2.50e+03 1.12e-02 2.53e+00 pdb=" CG TYR L 92 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 TYR L 92 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR L 92 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR L 92 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR L 92 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR L 92 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR L 92 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 449 " 0.019 2.00e-02 2.50e+03 1.06e-02 2.23e+00 pdb=" CG TYR E 449 " -0.008 2.00e-02 2.50e+03 pdb=" CD1 TYR E 449 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR E 449 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR E 449 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR E 449 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR E 449 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR E 449 " 0.017 2.00e-02 2.50e+03 ... (remaining 502 not shown) Histogram of nonbonded interaction distances: 2.55 - 3.02: 1515 3.02 - 3.49: 2477 3.49 - 3.96: 4310 3.96 - 4.43: 4896 4.43 - 4.90: 7917 Nonbonded interactions: 21115 Sorted by model distance: nonbonded pdb=" N ASP E 428 " pdb=" OD1 ASP E 428 " model vdw 2.553 3.120 nonbonded pdb=" N LYS E 462 " pdb=" O LYS E 462 " model vdw 2.609 2.496 nonbonded pdb=" N GLN L 3 " pdb=" OE1 GLN L 3 " model vdw 2.616 3.120 nonbonded pdb=" N THR H 76 " pdb=" N SER H 77 " model vdw 2.623 2.560 nonbonded pdb=" N ALA E 372 " pdb=" N SER E 373 " model vdw 2.627 2.560 ... (remaining 21110 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 ========== 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.570 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.740 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 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 : 0.010 0.057 2858 Z= 0.670 Angle : 1.245 7.544 3907 Z= 0.835 Chirality : 0.069 0.285 440 Planarity : 0.005 0.016 504 Dihedral : 9.309 63.153 948 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 0.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.45 % Allowed : 0.90 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.43), residues: 373 helix: -4.27 (0.43), residues: 26 sheet: 0.66 (0.46), residues: 126 loop : 0.27 (0.41), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.005 TRP L 35 PHE 0.016 0.003 PHE L 98 TYR 0.021 0.004 TYR L 92 ARG 0.003 0.000 ARG E 454 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 100 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8454 (mp10) cc_final: 0.8035 (tp40) REVERT: E 513 LEU cc_start: 0.8949 (mt) cc_final: 0.8631 (tt) outliers start: 1 outliers final: 1 residues processed: 100 average time/residue: 0.2018 time to fit residues: 23.1754 Evaluate side-chains 56 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 55 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 109 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 31 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 14 optimal weight: 0.4980 chunk 29 optimal weight: 0.7980 chunk 11 optimal weight: 0.3980 chunk 17 optimal weight: 0.0980 chunk 21 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 118 GLN L 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.098684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.090788 restraints weight = 7134.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.092566 restraints weight = 4159.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.093865 restraints weight = 2707.702| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 2858 Z= 0.341 Angle : 0.685 9.904 3907 Z= 0.358 Chirality : 0.049 0.204 440 Planarity : 0.004 0.027 504 Dihedral : 5.340 50.530 484 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 6.73 % Allowed : 15.70 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.42), residues: 373 helix: -3.64 (0.86), residues: 20 sheet: 0.70 (0.46), residues: 130 loop : 0.04 (0.40), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 47 PHE 0.019 0.002 PHE H 29 TYR 0.018 0.002 TYR H 95 ARG 0.005 0.001 ARG E 403 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8264 (mp10) cc_final: 0.8008 (tp40) REVERT: E 429 PHE cc_start: 0.8620 (t80) cc_final: 0.8412 (t80) REVERT: E 513 LEU cc_start: 0.9090 (mt) cc_final: 0.8830 (tt) REVERT: L 49 TYR cc_start: 0.8055 (p90) cc_final: 0.7702 (p90) REVERT: L 96 ARG cc_start: 0.7158 (ttt-90) cc_final: 0.6872 (ttm170) outliers start: 15 outliers final: 10 residues processed: 66 average time/residue: 0.1263 time to fit residues: 10.3712 Evaluate side-chains 61 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 88 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 35 optimal weight: 0.6980 chunk 20 optimal weight: 0.0970 chunk 29 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 30 optimal weight: 0.0980 chunk 34 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.095849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.087904 restraints weight = 7185.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.089719 restraints weight = 4145.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.091047 restraints weight = 2671.836| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 2858 Z= 0.298 Angle : 0.626 6.308 3907 Z= 0.328 Chirality : 0.045 0.140 440 Planarity : 0.004 0.027 504 Dihedral : 5.273 44.893 484 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 6.73 % Allowed : 19.28 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.43), residues: 373 helix: -2.90 (0.94), residues: 26 sheet: 0.71 (0.45), residues: 129 loop : -0.15 (0.41), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 PHE 0.030 0.002 PHE E 374 TYR 0.014 0.002 TYR E 423 ARG 0.002 0.000 ARG E 403 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8291 (mp10) cc_final: 0.8031 (tp40) REVERT: E 473 TYR cc_start: 0.8578 (t80) cc_final: 0.8315 (t80) REVERT: E 506 GLN cc_start: 0.7960 (mt0) cc_final: 0.7642 (mt0) REVERT: E 512 VAL cc_start: 0.9494 (t) cc_final: 0.9232 (m) REVERT: E 513 LEU cc_start: 0.9060 (mt) cc_final: 0.8744 (tt) REVERT: L 49 TYR cc_start: 0.8103 (p90) cc_final: 0.7606 (p90) outliers start: 15 outliers final: 11 residues processed: 65 average time/residue: 0.1131 time to fit residues: 9.2507 Evaluate side-chains 62 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 103 CYS Chi-restraints excluded: chain H residue 108 CYS Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain L residue 88 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 19 optimal weight: 0.8980 chunk 17 optimal weight: 0.0980 chunk 0 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 22 optimal weight: 0.4980 chunk 12 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 118 GLN L 34 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.091280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.083863 restraints weight = 7385.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.085568 restraints weight = 4254.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.086766 restraints weight = 2748.035| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.4243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 2858 Z= 0.385 Angle : 0.666 6.235 3907 Z= 0.350 Chirality : 0.046 0.141 440 Planarity : 0.005 0.061 504 Dihedral : 5.824 43.998 484 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 6.73 % Allowed : 19.28 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.42), residues: 373 helix: -2.72 (1.04), residues: 26 sheet: 1.01 (0.47), residues: 120 loop : -0.59 (0.39), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 47 PHE 0.022 0.003 PHE E 374 TYR 0.012 0.002 TYR H 95 ARG 0.004 0.001 ARG E 403 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: E 473 TYR cc_start: 0.8727 (t80) cc_final: 0.8422 (t80) REVERT: E 513 LEU cc_start: 0.9113 (mt) cc_final: 0.8767 (tt) REVERT: L 49 TYR cc_start: 0.8208 (p90) cc_final: 0.7771 (p90) outliers start: 15 outliers final: 15 residues processed: 62 average time/residue: 0.1144 time to fit residues: 9.0916 Evaluate side-chains 63 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 103 CYS Chi-restraints excluded: chain H residue 108 CYS Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 88 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 14 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 31 optimal weight: 0.0870 chunk 23 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 118 GLN L 34 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.090966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.083329 restraints weight = 7365.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.085082 restraints weight = 4122.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.086304 restraints weight = 2614.004| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.4705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.104 2858 Z= 0.403 Angle : 0.676 6.491 3907 Z= 0.355 Chirality : 0.047 0.143 440 Planarity : 0.005 0.032 504 Dihedral : 6.043 45.139 484 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 8.97 % Allowed : 18.39 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.42), residues: 373 helix: -2.80 (0.99), residues: 26 sheet: 0.97 (0.47), residues: 120 loop : -0.87 (0.38), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 47 PHE 0.021 0.002 PHE H 29 TYR 0.012 0.002 TYR E 423 ARG 0.005 0.001 ARG L 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 55 time to evaluate : 0.304 Fit side-chains revert: symmetry clash REVERT: H 29 PHE cc_start: 0.8271 (t80) cc_final: 0.7738 (t80) REVERT: E 467 ASP cc_start: 0.7445 (t0) cc_final: 0.6789 (p0) REVERT: E 473 TYR cc_start: 0.8805 (t80) cc_final: 0.8510 (t80) REVERT: E 513 LEU cc_start: 0.9088 (mt) cc_final: 0.8761 (tt) REVERT: L 49 TYR cc_start: 0.8296 (p90) cc_final: 0.7892 (p90) outliers start: 20 outliers final: 16 residues processed: 67 average time/residue: 0.1071 time to fit residues: 9.2485 Evaluate side-chains 68 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 52 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 103 CYS Chi-restraints excluded: chain H residue 108 CYS Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 391 CYS Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 11 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 15 optimal weight: 0.0970 chunk 14 optimal weight: 0.9990 chunk 18 optimal weight: 0.0870 chunk 24 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.091891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.084942 restraints weight = 7321.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.086518 restraints weight = 4266.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.087651 restraints weight = 2760.580| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.4911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 2858 Z= 0.297 Angle : 0.632 6.013 3907 Z= 0.329 Chirality : 0.046 0.139 440 Planarity : 0.004 0.029 504 Dihedral : 5.824 43.331 484 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 6.73 % Allowed : 21.52 % Favored : 71.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.42), residues: 373 helix: -2.57 (0.91), residues: 33 sheet: 0.90 (0.47), residues: 120 loop : -0.93 (0.40), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 47 PHE 0.013 0.002 PHE H 29 TYR 0.009 0.001 TYR E 423 ARG 0.002 0.000 ARG E 457 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: E 467 ASP cc_start: 0.7346 (t0) cc_final: 0.6898 (p0) REVERT: E 513 LEU cc_start: 0.9098 (mt) cc_final: 0.8757 (tt) REVERT: L 49 TYR cc_start: 0.8189 (p90) cc_final: 0.7821 (p90) outliers start: 15 outliers final: 14 residues processed: 64 average time/residue: 0.1160 time to fit residues: 9.3083 Evaluate side-chains 66 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 103 CYS Chi-restraints excluded: chain H residue 108 CYS Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 511 VAL Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 88 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 10 optimal weight: 0.5980 chunk 4 optimal weight: 0.0570 chunk 30 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 32 optimal weight: 0.3980 chunk 1 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 27 optimal weight: 0.1980 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 34 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.091840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.084106 restraints weight = 7474.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.085879 restraints weight = 4136.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.087160 restraints weight = 2613.892| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.5058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 2858 Z= 0.279 Angle : 0.629 7.135 3907 Z= 0.325 Chirality : 0.046 0.153 440 Planarity : 0.005 0.035 504 Dihedral : 5.770 42.599 484 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 6.73 % Allowed : 22.87 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.42), residues: 373 helix: -2.54 (0.84), residues: 39 sheet: 0.80 (0.46), residues: 120 loop : -0.96 (0.40), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 47 PHE 0.023 0.002 PHE H 29 TYR 0.010 0.001 TYR H 95 ARG 0.004 0.000 ARG L 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: H 29 PHE cc_start: 0.8107 (t80) cc_final: 0.7751 (t80) REVERT: E 467 ASP cc_start: 0.7350 (t0) cc_final: 0.6929 (p0) REVERT: E 513 LEU cc_start: 0.9111 (mt) cc_final: 0.8734 (tt) REVERT: L 49 TYR cc_start: 0.8184 (p90) cc_final: 0.7853 (p90) outliers start: 15 outliers final: 14 residues processed: 64 average time/residue: 0.1077 time to fit residues: 8.8660 Evaluate side-chains 68 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 103 CYS Chi-restraints excluded: chain H residue 108 CYS Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 32 TYR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 88 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 15 optimal weight: 0.0970 chunk 6 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 8 optimal weight: 0.0770 chunk 30 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 overall best weight: 0.5336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.091196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.084252 restraints weight = 7443.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.085817 restraints weight = 4305.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.086897 restraints weight = 2786.460| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.5288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 2858 Z= 0.326 Angle : 0.661 7.312 3907 Z= 0.340 Chirality : 0.046 0.139 440 Planarity : 0.005 0.029 504 Dihedral : 5.981 43.381 484 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 7.62 % Allowed : 23.32 % Favored : 69.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.42), residues: 373 helix: -2.59 (0.80), residues: 39 sheet: 0.74 (0.46), residues: 120 loop : -0.96 (0.41), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 47 PHE 0.016 0.002 PHE E 374 TYR 0.010 0.001 TYR L 32 ARG 0.008 0.001 ARG L 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 57 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: E 467 ASP cc_start: 0.7401 (t0) cc_final: 0.7058 (p0) REVERT: E 513 LEU cc_start: 0.9119 (mt) cc_final: 0.8758 (tt) REVERT: L 49 TYR cc_start: 0.8174 (p90) cc_final: 0.7875 (p90) outliers start: 17 outliers final: 17 residues processed: 66 average time/residue: 0.1162 time to fit residues: 9.7365 Evaluate side-chains 71 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 54 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 103 CYS Chi-restraints excluded: chain H residue 108 CYS Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 511 VAL Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 32 TYR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 16 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 15 optimal weight: 0.0980 chunk 1 optimal weight: 0.2980 chunk 10 optimal weight: 0.0070 chunk 24 optimal weight: 0.8980 chunk 32 optimal weight: 0.0970 chunk 25 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 27 optimal weight: 0.1980 overall best weight: 0.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.094823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.087706 restraints weight = 7309.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.089300 restraints weight = 4247.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.090456 restraints weight = 2763.473| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.5315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2858 Z= 0.177 Angle : 0.609 8.778 3907 Z= 0.303 Chirality : 0.045 0.133 440 Planarity : 0.004 0.026 504 Dihedral : 5.080 36.655 484 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 5.83 % Allowed : 25.56 % Favored : 68.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.43), residues: 373 helix: -3.17 (0.84), residues: 33 sheet: 0.83 (0.46), residues: 120 loop : -0.78 (0.42), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 436 PHE 0.017 0.002 PHE H 29 TYR 0.009 0.001 TYR H 95 ARG 0.002 0.000 ARG L 96 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: E 386 LYS cc_start: 0.9250 (mmtm) cc_final: 0.7532 (pttt) REVERT: E 467 ASP cc_start: 0.7405 (t0) cc_final: 0.6993 (p0) REVERT: E 513 LEU cc_start: 0.9103 (mt) cc_final: 0.8705 (tt) REVERT: L 49 TYR cc_start: 0.8054 (p90) cc_final: 0.7738 (p90) outliers start: 13 outliers final: 12 residues processed: 73 average time/residue: 0.1321 time to fit residues: 11.7722 Evaluate side-chains 70 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 103 CYS Chi-restraints excluded: chain H residue 108 CYS Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 32 TYR Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 27 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 10 optimal weight: 0.0170 chunk 13 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 28 optimal weight: 0.0010 chunk 29 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 4 optimal weight: 0.0060 chunk 20 optimal weight: 0.9990 overall best weight: 0.2440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.094350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.087268 restraints weight = 7296.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.088820 restraints weight = 4220.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.089936 restraints weight = 2755.815| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.5421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 2858 Z= 0.209 Angle : 0.616 7.700 3907 Z= 0.311 Chirality : 0.045 0.131 440 Planarity : 0.004 0.024 504 Dihedral : 4.796 34.700 482 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 5.38 % Allowed : 25.56 % Favored : 69.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.43), residues: 373 helix: -2.52 (0.79), residues: 39 sheet: 0.87 (0.46), residues: 120 loop : -0.72 (0.42), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 436 PHE 0.023 0.002 PHE E 429 TYR 0.013 0.001 TYR H 95 ARG 0.004 0.000 ARG L 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: E 386 LYS cc_start: 0.9224 (mmtm) cc_final: 0.7562 (pttt) REVERT: E 429 PHE cc_start: 0.8579 (t80) cc_final: 0.8187 (t80) REVERT: E 467 ASP cc_start: 0.7376 (t0) cc_final: 0.7046 (p0) REVERT: E 513 LEU cc_start: 0.9126 (mt) cc_final: 0.8757 (tt) REVERT: L 49 TYR cc_start: 0.8003 (p90) cc_final: 0.7679 (p90) outliers start: 12 outliers final: 12 residues processed: 68 average time/residue: 0.1277 time to fit residues: 10.6984 Evaluate side-chains 69 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 103 CYS Chi-restraints excluded: chain H residue 108 CYS Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 32 TYR Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 33 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 10 optimal weight: 0.2980 chunk 35 optimal weight: 0.9990 chunk 15 optimal weight: 0.0980 chunk 31 optimal weight: 0.9990 chunk 28 optimal weight: 0.3980 chunk 12 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.091863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.084693 restraints weight = 7333.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.086200 restraints weight = 4360.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.087296 restraints weight = 2895.263| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.5553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 2858 Z= 0.305 Angle : 0.657 7.337 3907 Z= 0.337 Chirality : 0.045 0.129 440 Planarity : 0.004 0.028 504 Dihedral : 5.274 38.428 482 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 6.28 % Allowed : 25.56 % Favored : 68.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.42), residues: 373 helix: -3.35 (0.78), residues: 33 sheet: 0.78 (0.47), residues: 114 loop : -0.88 (0.40), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 PHE 0.018 0.002 PHE E 429 TYR 0.016 0.001 TYR H 95 ARG 0.005 0.001 ARG H 98 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1362.15 seconds wall clock time: 25 minutes 8.44 seconds (1508.44 seconds total)