Starting phenix.real_space_refine on Wed Mar 5 16:59:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7r7n_24299/03_2025/7r7n_24299.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r7n_24299/03_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_24299/03_2025/7r7n_24299.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r7n_24299/03_2025/7r7n_24299.map" model { file = "/net/cci-nas-00/data/ceres_data/7r7n_24299/03_2025/7r7n_24299.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r7n_24299/03_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-5624/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: 3.40, per 1000 atoms: 1.22 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: 0.75 Conformation dependent library (CDL) restraints added in 325.5 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: 0.44 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: 0.80 Time building geometry restraints manager: 0.89 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: 7.690 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.370 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.280 ------------------------------------------------------------------------------- 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 : 0.269 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: 0.1855 time to fit residues: 21.2254 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 : 0.285 ------------------------------------------------------------------------------- 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: 0.0770 chunk 21 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN H 118 GLN L 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.098614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.090695 restraints weight = 7168.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.092475 restraints weight = 4204.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.093785 restraints weight = 2738.158| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 2858 Z= 0.332 Angle : 0.687 9.767 3907 Z= 0.358 Chirality : 0.049 0.179 440 Planarity : 0.004 0.033 504 Dihedral : 5.427 50.531 484 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 7.17 % Allowed : 15.25 % 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: -0.03 (0.42), residues: 373 helix: -3.45 (0.80), residues: 26 sheet: 0.87 (0.47), residues: 119 loop : -0.01 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 47 PHE 0.017 0.002 PHE H 29 TYR 0.020 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 75 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 59 time to evaluate : 0.288 Fit side-chains REVERT: H 3 GLN cc_start: 0.8233 (mp10) cc_final: 0.7987 (tp40) REVERT: E 513 LEU cc_start: 0.9090 (mt) cc_final: 0.8818 (tt) REVERT: L 49 TYR cc_start: 0.8051 (p90) cc_final: 0.7711 (p90) REVERT: L 96 ARG cc_start: 0.7172 (ttt-90) cc_final: 0.6587 (ttm110) outliers start: 16 outliers final: 10 residues processed: 68 average time/residue: 0.1317 time to fit residues: 10.9743 Evaluate side-chains 59 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.331 ------------------------------------------------------------------------------- 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: 0.7980 chunk 20 optimal weight: 0.0670 chunk 29 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 28 optimal weight: 0.4980 chunk 4 optimal weight: 0.0570 chunk 30 optimal weight: 0.0980 chunk 34 optimal weight: 0.7980 chunk 16 optimal weight: 0.3980 chunk 26 optimal weight: 0.4980 chunk 18 optimal weight: 0.7980 overall best weight: 0.2236 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.098847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.090693 restraints weight = 7122.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.092563 restraints weight = 4109.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.093887 restraints weight = 2655.201| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 2858 Z= 0.178 Angle : 0.575 5.957 3907 Z= 0.298 Chirality : 0.045 0.137 440 Planarity : 0.004 0.028 504 Dihedral : 4.827 44.097 484 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 5.38 % Allowed : 20.18 % Favored : 74.44 % 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 (0.43), residues: 373 helix: -3.05 (0.95), residues: 26 sheet: 0.68 (0.45), residues: 129 loop : 0.04 (0.41), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 PHE 0.029 0.002 PHE E 374 TYR 0.013 0.001 TYR E 423 ARG 0.004 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: 12 poor density : 59 time to evaluate : 0.308 Fit side-chains REVERT: H 3 GLN cc_start: 0.8234 (mp10) cc_final: 0.7964 (tp40) REVERT: E 513 LEU cc_start: 0.9039 (mt) cc_final: 0.8697 (tt) REVERT: L 49 TYR cc_start: 0.8038 (p90) cc_final: 0.7475 (p90) outliers start: 12 outliers final: 10 residues processed: 64 average time/residue: 0.1070 time to fit residues: 8.7457 Evaluate side-chains 64 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.302 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 17 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 12 optimal weight: 0.4980 chunk 28 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 14 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.092186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.084368 restraints weight = 7332.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.086130 restraints weight = 4171.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.087388 restraints weight = 2690.030| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 2858 Z= 0.395 Angle : 0.672 6.672 3907 Z= 0.353 Chirality : 0.046 0.140 440 Planarity : 0.005 0.052 504 Dihedral : 5.741 42.516 484 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 5.83 % Allowed : 21.08 % Favored : 73.09 % 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: -0.21 (0.43), residues: 373 helix: -2.73 (1.05), residues: 26 sheet: 0.99 (0.47), residues: 121 loop : -0.43 (0.40), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 47 PHE 0.024 0.003 PHE H 29 TYR 0.015 0.002 TYR H 95 ARG 0.005 0.001 ARG L 96 *********************** 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 66 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.305 Fit side-chains REVERT: H 3 GLN cc_start: 0.8316 (mp10) cc_final: 0.8080 (tp40) REVERT: E 442 ASP cc_start: 0.8858 (t0) cc_final: 0.8607 (t0) REVERT: E 513 LEU cc_start: 0.9176 (mt) cc_final: 0.8811 (tt) REVERT: L 49 TYR cc_start: 0.8197 (p90) cc_final: 0.7742 (p90) outliers start: 13 outliers final: 13 residues processed: 62 average time/residue: 0.1117 time to fit residues: 8.8373 Evaluate side-chains 63 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.341 ------------------------------------------------------------------------------- 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 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 88 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 14 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 30 optimal weight: 0.1980 chunk 31 optimal weight: 0.9990 chunk 23 optimal weight: 0.0970 chunk 35 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 29 optimal weight: 0.0050 chunk 33 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 overall best weight: 0.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN H 118 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.094542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.086763 restraints weight = 7204.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.088553 restraints weight = 4097.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.089846 restraints weight = 2622.293| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.4280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 2858 Z= 0.233 Angle : 0.592 5.956 3907 Z= 0.303 Chirality : 0.046 0.143 440 Planarity : 0.004 0.029 504 Dihedral : 5.207 40.415 484 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 5.83 % Allowed : 22.87 % Favored : 71.30 % 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: -0.23 (0.43), residues: 373 helix: -2.60 (1.08), residues: 26 sheet: 1.12 (0.48), residues: 118 loop : -0.54 (0.40), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 PHE 0.020 0.002 PHE E 374 TYR 0.012 0.001 TYR L 92 ARG 0.003 0.000 ARG E 403 *********************** 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 68 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8281 (mp10) cc_final: 0.8067 (tp40) REVERT: E 442 ASP cc_start: 0.8862 (t0) cc_final: 0.8659 (t0) REVERT: E 513 LEU cc_start: 0.9129 (mt) cc_final: 0.8768 (tt) REVERT: L 2 ILE cc_start: 0.7784 (mt) cc_final: 0.7487 (pt) REVERT: L 49 TYR cc_start: 0.8165 (p90) cc_final: 0.7758 (p90) outliers start: 13 outliers final: 13 residues processed: 62 average time/residue: 0.1115 time to fit residues: 8.9141 Evaluate side-chains 68 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 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 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 88 CYS 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: 0.9980 chunk 36 optimal weight: 0.4980 chunk 15 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 32 optimal weight: 0.0040 chunk 8 optimal weight: 0.5980 overall best weight: 0.6192 ------------------------------------------------------------------------------- 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 = 0.3343 r_free = 0.3343 target = 0.091105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.083753 restraints weight = 7332.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.085379 restraints weight = 4222.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.086597 restraints weight = 2731.833| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.4681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 2858 Z= 0.369 Angle : 0.649 6.273 3907 Z= 0.338 Chirality : 0.047 0.150 440 Planarity : 0.004 0.029 504 Dihedral : 5.847 40.937 484 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 8.07 % Allowed : 20.18 % 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: -0.46 (0.43), residues: 373 helix: -2.44 (1.09), residues: 26 sheet: 1.03 (0.49), residues: 114 loop : -0.75 (0.39), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 47 PHE 0.011 0.002 PHE E 377 TYR 0.012 0.001 TYR H 95 ARG 0.002 0.000 ARG L 96 *********************** 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 76 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 0.296 Fit side-chains revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8395 (mp10) cc_final: 0.8080 (tp40) REVERT: H 29 PHE cc_start: 0.8154 (t80) cc_final: 0.7761 (t80) REVERT: E 513 LEU cc_start: 0.9183 (mt) cc_final: 0.8814 (tt) REVERT: L 2 ILE cc_start: 0.7762 (mt) cc_final: 0.7490 (pt) REVERT: L 49 TYR cc_start: 0.8247 (p90) cc_final: 0.7867 (p90) outliers start: 18 outliers final: 15 residues processed: 69 average time/residue: 0.1157 time to fit residues: 10.0752 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 : 0.326 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 10 optimal weight: 0.0770 chunk 4 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 32 optimal weight: 0.0470 chunk 1 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 27 optimal weight: 0.0980 overall best weight: 0.3636 ------------------------------------------------------------------------------- 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 = 0.3372 r_free = 0.3372 target = 0.092477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.084721 restraints weight = 7430.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.086517 restraints weight = 4133.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.087742 restraints weight = 2602.094| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.4813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 2858 Z= 0.259 Angle : 0.629 6.430 3907 Z= 0.325 Chirality : 0.046 0.152 440 Planarity : 0.004 0.035 504 Dihedral : 5.564 39.277 484 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 5.38 % Allowed : 21.52 % Favored : 73.09 % 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 (0.43), residues: 373 helix: -2.35 (0.97), residues: 33 sheet: 0.98 (0.49), residues: 112 loop : -0.81 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 47 PHE 0.012 0.002 PHE H 29 TYR 0.011 0.001 TYR E 473 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: 12 poor density : 60 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8339 (mp10) cc_final: 0.8059 (tp40) REVERT: H 29 PHE cc_start: 0.8167 (t80) cc_final: 0.7690 (t80) REVERT: E 467 ASP cc_start: 0.7221 (t0) cc_final: 0.6945 (p0) REVERT: E 513 LEU cc_start: 0.9146 (mt) cc_final: 0.8793 (tt) REVERT: L 49 TYR cc_start: 0.8181 (p90) cc_final: 0.7755 (p90) outliers start: 12 outliers final: 10 residues processed: 66 average time/residue: 0.1143 time to fit residues: 9.4992 Evaluate side-chains 68 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.293 ------------------------------------------------------------------------------- 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 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 88 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 15 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 8 optimal weight: 0.2980 chunk 30 optimal weight: 0.5980 chunk 19 optimal weight: 0.1980 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 = 0.3351 r_free = 0.3351 target = 0.091180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.083366 restraints weight = 7456.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.085169 restraints weight = 4072.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.086406 restraints weight = 2540.177| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.5100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 2858 Z= 0.305 Angle : 0.636 6.175 3907 Z= 0.328 Chirality : 0.046 0.137 440 Planarity : 0.004 0.029 504 Dihedral : 5.368 30.648 482 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 5.83 % Allowed : 22.42 % 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: -0.63 (0.43), residues: 373 helix: -2.30 (0.95), residues: 33 sheet: 0.94 (0.48), residues: 114 loop : -0.86 (0.39), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 47 PHE 0.012 0.002 PHE H 29 TYR 0.011 0.001 TYR H 95 ARG 0.005 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 69 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.298 Fit side-chains revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8366 (mp10) cc_final: 0.8079 (tp40) REVERT: E 513 LEU cc_start: 0.9187 (mt) cc_final: 0.8793 (tt) REVERT: L 49 TYR cc_start: 0.8138 (p90) cc_final: 0.7761 (p90) outliers start: 13 outliers final: 13 residues processed: 63 average time/residue: 0.1209 time to fit residues: 9.6026 Evaluate side-chains 68 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.319 ------------------------------------------------------------------------------- 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 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 32 TYR Chi-restraints excluded: chain L residue 88 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 16 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 15 optimal weight: 0.0770 chunk 1 optimal weight: 1.9990 chunk 10 optimal weight: 0.0870 chunk 24 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.4116 ------------------------------------------------------------------------------- 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 = 0.3369 r_free = 0.3369 target = 0.092267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.084271 restraints weight = 7380.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.086130 restraints weight = 4047.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.087472 restraints weight = 2526.731| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.5221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 2858 Z= 0.281 Angle : 0.668 9.681 3907 Z= 0.342 Chirality : 0.046 0.178 440 Planarity : 0.005 0.040 504 Dihedral : 5.261 31.543 482 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 5.83 % Allowed : 24.22 % Favored : 69.96 % 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: -0.84 (0.42), residues: 373 helix: -2.52 (0.81), residues: 39 sheet: 0.79 (0.47), residues: 114 loop : -0.93 (0.40), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 47 PHE 0.015 0.002 PHE H 29 TYR 0.012 0.001 TYR H 95 ARG 0.005 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 71 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8303 (mp10) cc_final: 0.8072 (tp40) REVERT: E 513 LEU cc_start: 0.9189 (mt) cc_final: 0.8788 (tt) REVERT: L 49 TYR cc_start: 0.8189 (p90) cc_final: 0.7811 (p90) outliers start: 13 outliers final: 13 residues processed: 64 average time/residue: 0.1160 time to fit residues: 9.3550 Evaluate side-chains 68 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.303 ------------------------------------------------------------------------------- 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 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 32 TYR Chi-restraints excluded: chain L residue 88 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 27 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 28 optimal weight: 0.4980 chunk 29 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 20 optimal weight: 0.0970 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 = 0.3346 r_free = 0.3346 target = 0.090802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.083531 restraints weight = 7428.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.085157 restraints weight = 4292.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.086356 restraints weight = 2776.952| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.5414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 2858 Z= 0.366 Angle : 0.700 7.654 3907 Z= 0.362 Chirality : 0.047 0.148 440 Planarity : 0.005 0.036 504 Dihedral : 5.758 38.888 482 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 7.17 % Allowed : 24.22 % 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: -1.19 (0.41), residues: 373 helix: -3.42 (0.76), residues: 33 sheet: 0.69 (0.47), residues: 114 loop : -1.20 (0.38), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 47 PHE 0.013 0.002 PHE E 486 TYR 0.010 0.001 TYR H 95 ARG 0.005 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 71 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 55 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: E 513 LEU cc_start: 0.9194 (mt) cc_final: 0.8828 (tt) REVERT: L 49 TYR cc_start: 0.8223 (p90) cc_final: 0.7889 (p90) outliers start: 16 outliers final: 16 residues processed: 64 average time/residue: 0.1096 time to fit residues: 9.0024 Evaluate side-chains 66 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 50 time to evaluate : 0.306 ------------------------------------------------------------------------------- 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 468 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: 0.0970 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 31 optimal weight: 0.0370 chunk 28 optimal weight: 0.4980 chunk 12 optimal weight: 0.2980 chunk 16 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 overall best weight: 0.3056 ------------------------------------------------------------------------------- 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 = 0.3388 r_free = 0.3388 target = 0.093531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.085511 restraints weight = 7225.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.087261 restraints weight = 4071.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.088572 restraints weight = 2613.948| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.5526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 2858 Z= 0.229 Angle : 0.650 7.662 3907 Z= 0.329 Chirality : 0.045 0.136 440 Planarity : 0.004 0.034 504 Dihedral : 5.192 37.406 482 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 6.28 % Allowed : 25.11 % 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: -1.01 (0.42), residues: 373 helix: -3.29 (0.79), residues: 33 sheet: 0.71 (0.47), residues: 114 loop : -1.02 (0.39), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 PHE 0.013 0.002 PHE E 392 TYR 0.011 0.001 TYR E 473 ARG 0.003 0.000 ARG L 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1434.46 seconds wall clock time: 25 minutes 29.29 seconds (1529.29 seconds total)