Starting phenix.real_space_refine on Fri Dec 27 05:19:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jex_36202/12_2024/8jex_36202.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jex_36202/12_2024/8jex_36202.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jex_36202/12_2024/8jex_36202.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jex_36202/12_2024/8jex_36202.map" model { file = "/net/cci-nas-00/data/ceres_data/8jex_36202/12_2024/8jex_36202.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jex_36202/12_2024/8jex_36202.cif" } resolution = 3.1 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= 0.002 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: 3 Type Number sf(0) Gaussians C 1614 2.51 5 N 450 2.21 5 O 552 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 2616 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 377 Classifications: {'peptide': 55} Link IDs: {'TRANS': 54} Chain: "C" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: D, I, J, L, Q, B, G, H, K, P Time building chain proxies: 2.18, per 1000 atoms: 0.83 Number of scatterers: 2616 At special positions: 0 Unit cell: (112.05, 126.99, 31.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 552 8.00 N 450 7.00 C 1614 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-SER " NAG A 201 " - " SER A 87 " " NAG B 201 " - " SER B 87 " " NAG G 201 " - " SER G 87 " " NAG H 201 " - " SER H 87 " " NAG K 201 " - " SER K 87 " " NAG P 201 " - " SER P 87 " Time building additional restraints: 0.67 Conformation dependent library (CDL) restraints added in 323.3 milliseconds 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 660 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'H' and resid 40 through 44 Processing sheet with id=AA2, first strand: chain 'H' and resid 50 through 51 removed outlier: 6.458A pdb=" N HIS H 50 " --> pdb=" O GLY P 51 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N HIS P 50 " --> pdb=" O GLY G 51 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'H' and resid 63 through 66 Processing sheet with id=AA4, first strand: chain 'H' and resid 70 through 72 Processing sheet with id=AA5, first strand: chain 'H' and resid 76 through 79 removed outlier: 6.453A pdb=" N ALA H 76 " --> pdb=" O VAL P 77 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N GLN P 79 " --> pdb=" O ALA H 76 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ALA H 78 " --> pdb=" O GLN P 79 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ALA P 76 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N GLN G 79 " --> pdb=" O ALA P 76 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALA P 78 " --> pdb=" O GLN G 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 40 through 44 Processing sheet with id=AA7, first strand: chain 'B' and resid 50 through 51 removed outlier: 6.458A pdb=" N HIS B 50 " --> pdb=" O GLY K 51 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N HIS K 50 " --> pdb=" O GLY A 51 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 63 through 66 Processing sheet with id=AA9, first strand: chain 'B' and resid 70 through 72 Processing sheet with id=AB1, first strand: chain 'B' and resid 76 through 79 removed outlier: 6.452A pdb=" N ALA B 76 " --> pdb=" O VAL K 77 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N GLN K 79 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ALA B 78 " --> pdb=" O GLN K 79 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ALA K 76 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N GLN A 79 " --> pdb=" O ALA K 76 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALA K 78 " --> pdb=" O GLN A 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 36 hydrogen bonds defined for protein. 108 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: 0.53 Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.26: 468 1.26 - 1.33: 113 1.33 - 1.40: 355 1.40 - 1.48: 468 1.48 - 1.55: 1212 Bond restraints: 2616 Sorted by residual: bond pdb=" C7 NAG K 201 " pdb=" N2 NAG K 201 " ideal model delta sigma weight residual 1.346 1.452 -0.106 2.00e-02 2.50e+03 2.83e+01 bond pdb=" C7 NAG B 201 " pdb=" N2 NAG B 201 " ideal model delta sigma weight residual 1.346 1.452 -0.106 2.00e-02 2.50e+03 2.83e+01 bond pdb=" C7 NAG P 201 " pdb=" N2 NAG P 201 " ideal model delta sigma weight residual 1.346 1.452 -0.106 2.00e-02 2.50e+03 2.82e+01 bond pdb=" C7 NAG H 201 " pdb=" N2 NAG H 201 " ideal model delta sigma weight residual 1.346 1.452 -0.106 2.00e-02 2.50e+03 2.82e+01 bond pdb=" C7 NAG G 201 " pdb=" N2 NAG G 201 " ideal model delta sigma weight residual 1.346 1.452 -0.106 2.00e-02 2.50e+03 2.81e+01 ... (remaining 2611 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 3256 1.70 - 3.40: 182 3.40 - 5.10: 96 5.10 - 6.80: 0 6.80 - 8.51: 12 Bond angle restraints: 3546 Sorted by residual: angle pdb=" CB HIS G 50 " pdb=" CG HIS G 50 " pdb=" CD2 HIS G 50 " ideal model delta sigma weight residual 131.20 122.69 8.51 1.30e+00 5.92e-01 4.28e+01 angle pdb=" CB HIS B 50 " pdb=" CG HIS B 50 " pdb=" CD2 HIS B 50 " ideal model delta sigma weight residual 131.20 122.71 8.49 1.30e+00 5.92e-01 4.27e+01 angle pdb=" CB HIS K 50 " pdb=" CG HIS K 50 " pdb=" CD2 HIS K 50 " ideal model delta sigma weight residual 131.20 122.71 8.49 1.30e+00 5.92e-01 4.26e+01 angle pdb=" CB HIS H 50 " pdb=" CG HIS H 50 " pdb=" CD2 HIS H 50 " ideal model delta sigma weight residual 131.20 122.73 8.47 1.30e+00 5.92e-01 4.24e+01 angle pdb=" CB HIS P 50 " pdb=" CG HIS P 50 " pdb=" CD2 HIS P 50 " ideal model delta sigma weight residual 131.20 122.74 8.46 1.30e+00 5.92e-01 4.24e+01 ... (remaining 3541 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.32: 1320 9.32 - 18.63: 138 18.63 - 27.95: 90 27.95 - 37.26: 42 37.26 - 46.58: 12 Dihedral angle restraints: 1602 sinusoidal: 564 harmonic: 1038 Sorted by residual: dihedral pdb=" C LYS G 45 " pdb=" N LYS G 45 " pdb=" CA LYS G 45 " pdb=" CB LYS G 45 " ideal model delta harmonic sigma weight residual -122.60 -129.21 6.61 0 2.50e+00 1.60e-01 6.99e+00 dihedral pdb=" C LYS B 45 " pdb=" N LYS B 45 " pdb=" CA LYS B 45 " pdb=" CB LYS B 45 " ideal model delta harmonic sigma weight residual -122.60 -129.19 6.59 0 2.50e+00 1.60e-01 6.95e+00 dihedral pdb=" C LYS P 45 " pdb=" N LYS P 45 " pdb=" CA LYS P 45 " pdb=" CB LYS P 45 " ideal model delta harmonic sigma weight residual -122.60 -129.19 6.59 0 2.50e+00 1.60e-01 6.94e+00 ... (remaining 1599 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 314 0.044 - 0.089: 101 0.089 - 0.133: 53 0.133 - 0.178: 6 0.178 - 0.222: 12 Chirality restraints: 486 Sorted by residual: chirality pdb=" CA LYS B 45 " pdb=" N LYS B 45 " pdb=" C LYS B 45 " pdb=" CB LYS B 45 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA LYS G 45 " pdb=" N LYS G 45 " pdb=" C LYS G 45 " pdb=" CB LYS G 45 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CA LYS P 45 " pdb=" N LYS P 45 " pdb=" C LYS P 45 " pdb=" CB LYS P 45 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 483 not shown) Planarity restraints: 438 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU G 83 " -0.004 2.00e-02 2.50e+03 8.74e-03 7.64e-01 pdb=" C GLU G 83 " 0.015 2.00e-02 2.50e+03 pdb=" O GLU G 83 " -0.006 2.00e-02 2.50e+03 pdb=" N GLY G 84 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU P 83 " -0.004 2.00e-02 2.50e+03 8.70e-03 7.56e-01 pdb=" C GLU P 83 " 0.015 2.00e-02 2.50e+03 pdb=" O GLU P 83 " -0.006 2.00e-02 2.50e+03 pdb=" N GLY P 84 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU K 83 " 0.004 2.00e-02 2.50e+03 8.57e-03 7.34e-01 pdb=" C GLU K 83 " -0.015 2.00e-02 2.50e+03 pdb=" O GLU K 83 " 0.006 2.00e-02 2.50e+03 pdb=" N GLY K 84 " 0.005 2.00e-02 2.50e+03 ... (remaining 435 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 1388 2.98 - 3.46: 2214 3.46 - 3.94: 3618 3.94 - 4.42: 4179 4.42 - 4.90: 8243 Nonbonded interactions: 19642 Sorted by model distance: nonbonded pdb=" O5 NAG B 201 " pdb=" O6 NAG B 201 " model vdw 2.505 2.432 nonbonded pdb=" O5 NAG H 201 " pdb=" O6 NAG H 201 " model vdw 2.505 2.432 nonbonded pdb=" O5 NAG G 201 " pdb=" O6 NAG G 201 " model vdw 2.505 2.432 nonbonded pdb=" O5 NAG K 201 " pdb=" O6 NAG K 201 " model vdw 2.505 2.432 nonbonded pdb=" O5 NAG P 201 " pdb=" O6 NAG P 201 " model vdw 2.506 2.432 ... (remaining 19637 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'G' selection = chain 'H' selection = chain 'K' selection = chain 'P' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'I' selection = chain 'J' selection = chain 'L' selection = chain 'Q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.480 Find NCS groups from input model: 0.130 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 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 : 0.012 0.106 2616 Z= 0.817 Angle : 1.131 8.505 3546 Z= 0.701 Chirality : 0.062 0.222 486 Planarity : 0.002 0.009 438 Dihedral : 12.572 46.580 942 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.00 % Allowed : 12.82 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.98 (0.27), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.79 (0.20), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS K 50 TYR 0.003 0.001 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.293 Fit side-chains REVERT: G 58 LYS cc_start: 0.8346 (ttmt) cc_final: 0.8080 (mtpt) REVERT: A 58 LYS cc_start: 0.8325 (ttmt) cc_final: 0.8115 (mtpt) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.2303 time to fit residues: 12.0388 Evaluate side-chains 45 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 0.4980 chunk 27 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 2616 Z= 0.126 Angle : 0.460 2.760 3546 Z= 0.243 Chirality : 0.048 0.116 486 Planarity : 0.001 0.008 438 Dihedral : 6.391 32.618 504 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.43 % Allowed : 16.24 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.40 (0.30), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.35 (0.23), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 50 TYR 0.006 0.001 TYR K 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.286 Fit side-chains REVERT: H 43 LYS cc_start: 0.8705 (mptt) cc_final: 0.8289 (mmtm) REVERT: B 43 LYS cc_start: 0.8779 (mptt) cc_final: 0.8393 (mtmm) REVERT: A 58 LYS cc_start: 0.8363 (ttmt) cc_final: 0.8125 (mtpt) outliers start: 1 outliers final: 1 residues processed: 44 average time/residue: 0.1890 time to fit residues: 9.6110 Evaluate side-chains 45 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 59 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 0.0020 chunk 18 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 overall best weight: 3.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.023 2616 Z= 0.314 Angle : 0.562 3.773 3546 Z= 0.293 Chirality : 0.050 0.138 486 Planarity : 0.002 0.007 438 Dihedral : 5.016 19.410 504 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 0.43 % Allowed : 18.38 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.17 (0.32), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.17 (0.25), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS H 50 TYR 0.007 0.001 TYR P 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.285 Fit side-chains REVERT: H 58 LYS cc_start: 0.8282 (ttmt) cc_final: 0.7994 (mtpt) REVERT: B 43 LYS cc_start: 0.8776 (mptt) cc_final: 0.8454 (mtmm) outliers start: 1 outliers final: 1 residues processed: 38 average time/residue: 0.2161 time to fit residues: 9.4643 Evaluate side-chains 39 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 59 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 5.9990 chunk 13 optimal weight: 0.2980 chunk 18 optimal weight: 8.9990 chunk 27 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 14 optimal weight: 0.0970 chunk 25 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 2616 Z= 0.241 Angle : 0.484 3.474 3546 Z= 0.259 Chirality : 0.049 0.128 486 Planarity : 0.002 0.007 438 Dihedral : 3.661 11.708 504 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.14 % Allowed : 18.38 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.92 (0.36), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.98 (0.27), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS H 50 TYR 0.005 0.001 TYR K 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.233 Fit side-chains REVERT: H 58 LYS cc_start: 0.8296 (ttmt) cc_final: 0.8000 (mtpp) outliers start: 5 outliers final: 5 residues processed: 33 average time/residue: 0.2090 time to fit residues: 8.0020 Evaluate side-chains 38 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain A residue 59 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 20 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 0.0050 chunk 26 optimal weight: 7.9990 chunk 7 optimal weight: 0.0770 chunk 9 optimal weight: 0.7980 chunk 5 optimal weight: 7.9990 chunk 17 optimal weight: 4.9990 overall best weight: 2.3756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 2616 Z= 0.218 Angle : 0.465 3.565 3546 Z= 0.248 Chirality : 0.049 0.127 486 Planarity : 0.001 0.005 438 Dihedral : 3.538 11.432 504 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 1.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.99 % Allowed : 20.51 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.67 (0.38), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.79 (0.29), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS H 50 TYR 0.005 0.001 TYR P 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.250 Fit side-chains REVERT: H 58 LYS cc_start: 0.8306 (ttmt) cc_final: 0.8025 (mtpp) outliers start: 7 outliers final: 7 residues processed: 37 average time/residue: 0.1693 time to fit residues: 7.4189 Evaluate side-chains 41 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 37 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain A residue 59 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 chunk 16 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.017 2616 Z= 0.248 Angle : 0.492 3.769 3546 Z= 0.261 Chirality : 0.049 0.128 486 Planarity : 0.002 0.004 438 Dihedral : 3.647 12.231 504 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 1.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 4.70 % Allowed : 23.08 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.57 (0.39), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.71 (0.29), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS H 50 TYR 0.006 0.001 TYR P 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 33 time to evaluate : 0.260 Fit side-chains REVERT: H 58 LYS cc_start: 0.8315 (ttmt) cc_final: 0.8031 (mtpp) outliers start: 11 outliers final: 11 residues processed: 39 average time/residue: 0.1719 time to fit residues: 7.8960 Evaluate side-chains 44 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 33 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain P residue 37 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 59 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 8.9990 chunk 24 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 18 optimal weight: 7.9990 chunk 17 optimal weight: 0.1980 chunk 13 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 14 optimal weight: 0.0060 overall best weight: 2.0402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 2616 Z= 0.188 Angle : 0.423 3.045 3546 Z= 0.230 Chirality : 0.048 0.126 486 Planarity : 0.001 0.004 438 Dihedral : 3.300 11.119 504 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 1.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 5.13 % Allowed : 23.08 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.41 (0.40), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.59 (0.30), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 50 TYR 0.005 0.001 TYR P 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 31 time to evaluate : 0.277 Fit side-chains outliers start: 12 outliers final: 11 residues processed: 37 average time/residue: 0.1312 time to fit residues: 5.9020 Evaluate side-chains 42 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 31 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain P residue 37 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 59 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 4.9990 chunk 22 optimal weight: 8.9990 chunk 26 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 chunk 25 optimal weight: 9.9990 chunk 16 optimal weight: 8.9990 chunk 11 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 chunk 24 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 2616 Z= 0.213 Angle : 0.452 3.719 3546 Z= 0.242 Chirality : 0.049 0.125 486 Planarity : 0.001 0.004 438 Dihedral : 3.454 11.582 504 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 1.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 5.13 % Allowed : 23.50 % Favored : 71.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.32 (0.40), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.52 (0.31), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 50 TYR 0.006 0.001 TYR P 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 31 time to evaluate : 0.275 Fit side-chains REVERT: H 58 LYS cc_start: 0.8294 (ttmt) cc_final: 0.8014 (mtpp) outliers start: 12 outliers final: 12 residues processed: 38 average time/residue: 0.1661 time to fit residues: 7.4974 Evaluate side-chains 43 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 31 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain P residue 37 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 59 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 19 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.009 2616 Z= 0.096 Angle : 0.358 4.115 3546 Z= 0.197 Chirality : 0.047 0.123 486 Planarity : 0.001 0.004 438 Dihedral : 2.951 9.647 504 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 1.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.71 % Allowed : 27.78 % Favored : 70.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (0.41), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.36 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 50 TYR 0.003 0.001 TYR K 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.283 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 34 average time/residue: 0.1729 time to fit residues: 7.0425 Evaluate side-chains 34 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 42 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 chunk 6 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 4 optimal weight: 0.0770 chunk 20 optimal weight: 2.9990 chunk 1 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 overall best weight: 2.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.013 2616 Z= 0.187 Angle : 0.417 4.095 3546 Z= 0.224 Chirality : 0.048 0.125 486 Planarity : 0.001 0.004 438 Dihedral : 3.213 10.814 504 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.71 % Allowed : 27.78 % Favored : 70.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.05 (0.42), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.32 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 50 TYR 0.006 0.001 TYR K 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.273 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 35 average time/residue: 0.1693 time to fit residues: 7.1013 Evaluate side-chains 35 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 42 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 0.8980 chunk 16 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 11 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 28 optimal weight: 4.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- 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 = 0.4259 r_free = 0.4259 target = 0.133511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.106312 restraints weight = 3515.815| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 3.25 r_work: 0.3772 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.017 2616 Z= 0.245 Angle : 0.468 4.395 3546 Z= 0.249 Chirality : 0.049 0.124 486 Planarity : 0.001 0.004 438 Dihedral : 3.516 11.720 504 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.14 % Allowed : 28.21 % Favored : 69.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (0.41), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.35 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 50 TYR 0.007 0.001 TYR K 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1121.23 seconds wall clock time: 20 minutes 43.76 seconds (1243.76 seconds total)