Starting phenix.real_space_refine on Fri Aug 2 13:10:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zwh_60527/08_2024/8zwh_60527.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zwh_60527/08_2024/8zwh_60527.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zwh_60527/08_2024/8zwh_60527.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zwh_60527/08_2024/8zwh_60527.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zwh_60527/08_2024/8zwh_60527.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zwh_60527/08_2024/8zwh_60527.cif" } resolution = 2.5 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= 0.002 sd= 0.004 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 1410 2.51 5 N 408 2.21 5 O 450 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 2268 Number of models: 1 Model: "" Number of chains: 6 Chain: "E" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Chain: "B" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Chain: "D" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Chain: "A" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Chain: "F" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Chain: "C" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Time building chain proxies: 1.94, per 1000 atoms: 0.86 Number of scatterers: 2268 At special positions: 0 Unit cell: (82.17, 94.62, 35.69, 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 450 8.00 N 408 7.00 C 1410 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.70 Conformation dependent library (CDL) restraints added in 415.5 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: 564 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 30.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 46 through 47 Processing sheet with id=AA2, first strand: chain 'D' and resid 61 through 66 removed outlier: 6.406A pdb=" N GLU E 61 " --> pdb=" O GLN D 62 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N THR D 64 " --> pdb=" O GLU E 61 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N VAL E 63 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N VAL D 66 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ASN E 65 " --> pdb=" O VAL D 66 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 69 through 71 removed outlier: 6.699A pdb=" N VAL E 70 " --> pdb=" O VAL D 71 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 75 through 79 removed outlier: 6.577A pdb=" N THR E 75 " --> pdb=" O ALA F 76 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ALA F 78 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N VAL E 77 " --> pdb=" O ALA F 78 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 90 through 94 removed outlier: 8.565A pdb=" N ALA E 90 " --> pdb=" O ALA D 91 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N GLY D 93 " --> pdb=" O ALA E 90 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N THR E 92 " --> pdb=" O GLY D 93 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N GLY F 93 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N PHE E 94 " --> pdb=" O GLY F 93 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 46 through 48 removed outlier: 6.039A pdb=" N GLY B 47 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 61 through 66 removed outlier: 6.433A pdb=" N GLU B 61 " --> pdb=" O GLN A 62 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N THR A 64 " --> pdb=" O GLU B 61 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N VAL B 63 " --> pdb=" O THR A 64 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N VAL A 66 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ASN B 65 " --> pdb=" O VAL A 66 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 69 through 71 removed outlier: 6.687A pdb=" N VAL B 70 " --> pdb=" O VAL A 71 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 75 through 79 removed outlier: 6.656A pdb=" N THR B 75 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ALA C 78 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N VAL B 77 " --> pdb=" O ALA C 78 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 90 through 94 removed outlier: 8.535A pdb=" N ALA B 90 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N GLY A 93 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N THR B 92 " --> pdb=" O GLY A 93 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ALA B 91 " --> pdb=" O ALA C 90 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N THR C 92 " --> pdb=" O ALA B 91 " (cutoff:3.500A) 31 hydrogen bonds defined for protein. 93 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: 0.47 Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.28: 402 1.28 - 1.35: 360 1.35 - 1.41: 60 1.41 - 1.48: 384 1.48 - 1.54: 1068 Bond restraints: 2274 Sorted by residual: bond pdb=" CB VAL D 49 " pdb=" CG2 VAL D 49 " ideal model delta sigma weight residual 1.521 1.434 0.087 3.30e-02 9.18e+02 7.00e+00 bond pdb=" CB VAL C 49 " pdb=" CG2 VAL C 49 " ideal model delta sigma weight residual 1.521 1.434 0.087 3.30e-02 9.18e+02 6.98e+00 bond pdb=" CB VAL B 49 " pdb=" CG2 VAL B 49 " ideal model delta sigma weight residual 1.521 1.434 0.087 3.30e-02 9.18e+02 6.97e+00 bond pdb=" CB VAL E 49 " pdb=" CG2 VAL E 49 " ideal model delta sigma weight residual 1.521 1.435 0.086 3.30e-02 9.18e+02 6.86e+00 bond pdb=" CB VAL F 49 " pdb=" CG2 VAL F 49 " ideal model delta sigma weight residual 1.521 1.435 0.086 3.30e-02 9.18e+02 6.86e+00 ... (remaining 2269 not shown) Histogram of bond angle deviations from ideal: 105.34 - 110.56: 816 110.56 - 115.79: 791 115.79 - 121.02: 797 121.02 - 126.24: 656 126.24 - 131.47: 6 Bond angle restraints: 3066 Sorted by residual: angle pdb=" C VAL C 52 " pdb=" N ALA C 53 " pdb=" CA ALA C 53 " ideal model delta sigma weight residual 122.67 119.51 3.16 1.73e+00 3.34e-01 3.33e+00 angle pdb=" C VAL B 52 " pdb=" N ALA B 53 " pdb=" CA ALA B 53 " ideal model delta sigma weight residual 122.67 119.56 3.11 1.73e+00 3.34e-01 3.23e+00 angle pdb=" C VAL D 52 " pdb=" N ALA D 53 " pdb=" CA ALA D 53 " ideal model delta sigma weight residual 122.67 119.57 3.10 1.73e+00 3.34e-01 3.21e+00 angle pdb=" N GLY D 93 " pdb=" CA GLY D 93 " pdb=" C GLY D 93 " ideal model delta sigma weight residual 113.18 108.94 4.24 2.37e+00 1.78e-01 3.21e+00 angle pdb=" C LYS F 80 " pdb=" N THR F 81 " pdb=" CA THR F 81 " ideal model delta sigma weight residual 121.86 119.04 2.82 1.58e+00 4.01e-01 3.19e+00 ... (remaining 3061 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 6.98: 1074 6.98 - 13.96: 168 13.96 - 20.94: 60 20.94 - 27.92: 24 27.92 - 34.91: 18 Dihedral angle restraints: 1344 sinusoidal: 456 harmonic: 888 Sorted by residual: dihedral pdb=" CA VAL A 49 " pdb=" C VAL A 49 " pdb=" N HIS A 50 " pdb=" CA HIS A 50 " ideal model delta harmonic sigma weight residual 180.00 157.40 22.60 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA VAL C 49 " pdb=" C VAL C 49 " pdb=" N HIS C 50 " pdb=" CA HIS C 50 " ideal model delta harmonic sigma weight residual 180.00 157.40 22.60 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA VAL B 49 " pdb=" C VAL B 49 " pdb=" N HIS B 50 " pdb=" CA HIS B 50 " ideal model delta harmonic sigma weight residual 180.00 157.41 22.59 0 5.00e+00 4.00e-02 2.04e+01 ... (remaining 1341 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.032: 143 0.032 - 0.064: 140 0.064 - 0.096: 59 0.096 - 0.128: 42 0.128 - 0.159: 18 Chirality restraints: 402 Sorted by residual: chirality pdb=" CB VAL C 95 " pdb=" CA VAL C 95 " pdb=" CG1 VAL C 95 " pdb=" CG2 VAL C 95 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.34e-01 chirality pdb=" CB VAL B 95 " pdb=" CA VAL B 95 " pdb=" CG1 VAL B 95 " pdb=" CG2 VAL B 95 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.23e-01 chirality pdb=" CB VAL F 95 " pdb=" CA VAL F 95 " pdb=" CG1 VAL F 95 " pdb=" CG2 VAL F 95 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.21e-01 ... (remaining 399 not shown) Planarity restraints: 384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 94 " 0.011 2.00e-02 2.50e+03 8.65e-03 1.31e+00 pdb=" CG PHE A 94 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 PHE A 94 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 94 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 94 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 94 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 94 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 94 " -0.012 2.00e-02 2.50e+03 8.58e-03 1.29e+00 pdb=" CG PHE E 94 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 PHE E 94 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE E 94 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE E 94 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE E 94 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE E 94 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 94 " 0.011 2.00e-02 2.50e+03 8.55e-03 1.28e+00 pdb=" CG PHE B 94 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 PHE B 94 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE B 94 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 94 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 94 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE B 94 " 0.002 2.00e-02 2.50e+03 ... (remaining 381 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 649 2.81 - 3.33: 1787 3.33 - 3.85: 3495 3.85 - 4.38: 3536 4.38 - 4.90: 7673 Nonbonded interactions: 17140 Sorted by model distance: nonbonded pdb=" OD1 ASP C 98 " pdb=" N GLN C 99 " model vdw 2.284 3.120 nonbonded pdb=" OD1 ASP B 98 " pdb=" N GLN B 99 " model vdw 2.285 3.120 nonbonded pdb=" OD1 ASP E 98 " pdb=" N GLN E 99 " model vdw 2.285 3.120 nonbonded pdb=" OD1 ASP D 98 " pdb=" N GLN D 99 " model vdw 2.285 3.120 nonbonded pdb=" OD1 ASP F 98 " pdb=" N GLN F 99 " model vdw 2.286 3.120 ... (remaining 17135 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 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.630 Find NCS groups from input model: 0.080 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: 0.010 Load rotamer database and sin/cos tables:14.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 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 : 0.011 0.087 2274 Z= 0.762 Angle : 0.907 4.244 3066 Z= 0.510 Chirality : 0.062 0.159 402 Planarity : 0.003 0.009 384 Dihedral : 9.450 34.906 780 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 18.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % 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: -4.12 (0.32), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.13 (0.25), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 50 PHE 0.019 0.006 PHE A 94 *********************** 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 16 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.268 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 1.7124 time to fit residues: 28.0939 Evaluate side-chains 1 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1 time to evaluate : 0.270 ------------------------------------------------------------------------------- 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: 20.0000 chunk 22 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 7 optimal weight: 6.9990 chunk 15 optimal weight: 30.0000 chunk 23 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 14 optimal weight: 20.0000 chunk 17 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2274 Z= 0.230 Angle : 0.589 5.113 3066 Z= 0.318 Chirality : 0.052 0.140 402 Planarity : 0.002 0.008 384 Dihedral : 5.992 17.078 324 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.00 % Allowed : 14.04 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % 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: -3.36 (0.37), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.55 (0.28), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 50 PHE 0.012 0.003 PHE E 94 *********************** 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 2 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.270 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 1.2970 time to fit residues: 3.0434 Evaluate side-chains 2 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 30.0000 chunk 18 optimal weight: 9.9990 chunk 7 optimal weight: 20.0000 chunk 27 optimal weight: 20.0000 chunk 29 optimal weight: 0.9990 chunk 24 optimal weight: 20.0000 chunk 9 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 26 optimal weight: 0.0020 chunk 20 optimal weight: 4.9990 chunk 14 optimal weight: 0.0980 overall best weight: 2.4194 ------------------------------------------------------------------------------- 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: 0.8139 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 2274 Z= 0.133 Angle : 0.460 4.552 3066 Z= 0.251 Chirality : 0.051 0.140 402 Planarity : 0.001 0.008 384 Dihedral : 5.206 13.768 324 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.07 % Allowed : 13.16 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % 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: -3.16 (0.39), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.40 (0.29), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 50 PHE 0.008 0.002 PHE B 94 *********************** 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 9 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 2 time to evaluate : 0.272 Fit side-chains outliers start: 7 outliers final: 1 residues processed: 9 average time/residue: 1.7517 time to fit residues: 16.3350 Evaluate side-chains 3 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 2 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 20.0000 chunk 13 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 27 optimal weight: 20.0000 chunk 28 optimal weight: 5.9990 chunk 14 optimal weight: 20.0000 chunk 25 optimal weight: 8.9990 chunk 7 optimal weight: 8.9990 chunk 24 optimal weight: 30.0000 chunk 16 optimal weight: 8.9990 chunk 0 optimal weight: 50.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 2274 Z= 0.372 Angle : 0.580 5.490 3066 Z= 0.317 Chirality : 0.052 0.139 402 Planarity : 0.002 0.010 384 Dihedral : 5.960 19.478 324 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 2.19 % Allowed : 11.84 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % 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: -3.43 (0.38), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.61 (0.29), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 50 PHE 0.014 0.003 PHE B 94 *********************** 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 6 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1 time to evaluate : 0.284 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 6 average time/residue: 0.4839 time to fit residues: 3.4315 Evaluate side-chains 5 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 0 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain F residue 52 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 0.0980 chunk 11 optimal weight: 7.9990 chunk 24 optimal weight: 30.0000 chunk 20 optimal weight: 30.0000 chunk 0 optimal weight: 30.0000 chunk 14 optimal weight: 0.0060 chunk 26 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 9 optimal weight: 30.0000 chunk 5 optimal weight: 50.0000 chunk 17 optimal weight: 0.9980 overall best weight: 2.0200 ------------------------------------------------------------------------------- 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: 0.8132 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2274 Z= 0.113 Angle : 0.422 4.752 3066 Z= 0.231 Chirality : 0.050 0.141 402 Planarity : 0.001 0.009 384 Dihedral : 5.138 14.016 324 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.00 % Allowed : 14.47 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % 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: -3.28 (0.39), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.49 (0.30), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS A 50 PHE 0.007 0.002 PHE B 94 *********************** 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 3 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.267 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 1.8260 time to fit residues: 5.9383 Evaluate side-chains 0 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 20.0000 chunk 29 optimal weight: 9.9990 chunk 24 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 2 optimal weight: 20.0000 chunk 9 optimal weight: 10.0000 chunk 15 optimal weight: 40.0000 chunk 27 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 21 optimal weight: 3.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- 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: 0.8146 moved from start: 0.3911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 2274 Z= 0.148 Angle : 0.435 4.981 3066 Z= 0.237 Chirality : 0.050 0.138 402 Planarity : 0.002 0.017 384 Dihedral : 5.007 14.605 324 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 2.19 % Allowed : 12.28 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % 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: -3.19 (0.40), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.43 (0.31), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 50 PHE 0.009 0.002 PHE B 94 *********************** 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 5 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 0 time to evaluate : 0.289 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 5 average time/residue: 0.0503 time to fit residues: 0.7402 Evaluate side-chains 3 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 0 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain F residue 52 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 18 optimal weight: 20.0000 chunk 17 optimal weight: 0.0970 chunk 13 optimal weight: 9.9990 chunk 11 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 5 optimal weight: 50.0000 chunk 19 optimal weight: 9.9990 chunk 14 optimal weight: 20.0000 overall best weight: 5.4186 ------------------------------------------------------------------------------- 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: 0.8176 moved from start: 0.3952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2274 Z= 0.245 Angle : 0.482 5.123 3066 Z= 0.263 Chirality : 0.051 0.139 402 Planarity : 0.002 0.014 384 Dihedral : 5.399 16.735 324 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 2.63 % Allowed : 11.40 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % 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: -3.29 (0.39), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.50 (0.30), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 50 PHE 0.010 0.002 PHE E 94 *********************** 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 6 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 0 time to evaluate : 0.355 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 6 average time/residue: 0.0411 time to fit residues: 0.7891 Evaluate side-chains 4 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 0 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain F residue 52 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 20.0000 chunk 22 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 chunk 25 optimal weight: 40.0000 chunk 16 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- 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: 0.8158 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2274 Z= 0.182 Angle : 0.443 5.105 3066 Z= 0.242 Chirality : 0.050 0.139 402 Planarity : 0.002 0.012 384 Dihedral : 5.100 15.536 324 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 0.88 % Allowed : 13.60 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % 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: -3.25 (0.40), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.47 (0.30), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 50 PHE 0.007 0.002 PHE A 94 *********************** 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 3 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1 time to evaluate : 0.268 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 3 average time/residue: 0.0507 time to fit residues: 0.6136 Evaluate side-chains 2 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 0 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain F residue 52 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 10.0000 chunk 17 optimal weight: 20.0000 chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 29 optimal weight: 30.0000 chunk 27 optimal weight: 7.9990 chunk 23 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 14 optimal weight: 20.0000 chunk 25 optimal weight: 0.2980 overall best weight: 3.9584 ------------------------------------------------------------------------------- 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: 0.8161 moved from start: 0.4336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2274 Z= 0.185 Angle : 0.441 5.131 3066 Z= 0.242 Chirality : 0.050 0.139 402 Planarity : 0.001 0.011 384 Dihedral : 5.092 15.680 324 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 1.32 % Allowed : 14.04 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % 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: -3.19 (0.40), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.43 (0.30), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 50 PHE 0.008 0.002 PHE A 94 *********************** 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 3 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 0 time to evaluate : 0.278 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 3 average time/residue: 0.0525 time to fit residues: 0.6253 Evaluate side-chains 3 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 0 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain F residue 52 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 20.0000 chunk 21 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 6 optimal weight: 20.0000 chunk 23 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 24 optimal weight: 20.0000 chunk 4 optimal weight: 20.0000 chunk 20 optimal weight: 30.0000 chunk 1 optimal weight: 20.0000 chunk 17 optimal weight: 6.9990 overall best weight: 6.1992 ------------------------------------------------------------------------------- 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: 0.8191 moved from start: 0.4349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2274 Z= 0.280 Angle : 0.502 5.491 3066 Z= 0.274 Chirality : 0.051 0.139 402 Planarity : 0.002 0.010 384 Dihedral : 5.499 18.293 324 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 1.75 % Allowed : 13.60 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % 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: -3.24 (0.39), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.46 (0.30), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 50 PHE 0.010 0.002 PHE A 94 ********************** 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 6 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 2 time to evaluate : 0.263 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 6 average time/residue: 0.7967 time to fit residues: 5.2480 Evaluate side-chains 4 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 0 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain F residue 52 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 20.0000 chunk 16 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 19 optimal weight: 40.0000 chunk 18 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 29 optimal weight: 30.0000 chunk 1 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 = 0.4759 r_free = 0.4759 target = 0.104672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.087599 restraints weight = 7207.550| |-----------------------------------------------------------------------------| r_work (start): 0.4520 rms_B_bonded: 3.66 r_work: 0.4380 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.4380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.4630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2274 Z= 0.168 Angle : 0.451 4.963 3066 Z= 0.246 Chirality : 0.050 0.140 402 Planarity : 0.002 0.014 384 Dihedral : 5.042 15.876 324 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.32 % Allowed : 14.47 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % 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: -3.15 (0.40), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.40 (0.30), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 50 PHE 0.008 0.002 PHE A 94 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 944.83 seconds wall clock time: 17 minutes 18.64 seconds (1038.64 seconds total)