Starting phenix.real_space_refine on Wed Mar 5 15:20:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zwh_60527/03_2025/8zwh_60527.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zwh_60527/03_2025/8zwh_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/cci-nas-00/data/ceres_data/8zwh_60527/03_2025/8zwh_60527.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zwh_60527/03_2025/8zwh_60527.map" model { file = "/net/cci-nas-00/data/ceres_data/8zwh_60527/03_2025/8zwh_60527.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zwh_60527/03_2025/8zwh_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. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 2268 Number of models: 1 Model: "" Number of chains: 1 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} Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 1.37, per 1000 atoms: 0.60 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.55 Conformation dependent library (CDL) restraints added in 290.7 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: 0.32 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: 0.45 Time building geometry restraints manager: 0.66 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: 0.00 - 0.85: 2349 0.85 - 1.70: 476 1.70 - 2.55: 158 2.55 - 3.40: 65 3.40 - 4.24: 18 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' 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: 0.780 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.880 Find NCS groups from input model: 0.050 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:13.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.170 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.260 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 1.7554 time to fit residues: 28.7646 Evaluate side-chains 1 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1 time to evaluate : 0.237 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4721 r_free = 0.4721 target = 0.102408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.084654 restraints weight = 7212.409| |-----------------------------------------------------------------------------| r_work (start): 0.4439 rms_B_bonded: 3.79 r_work: 0.4347 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.4347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 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 to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.248 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 1.3690 time to fit residues: 3.1818 Evaluate side-chains 2 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 20.0000 chunk 17 optimal weight: 8.9990 chunk 11 optimal weight: 0.8980 chunk 3 optimal weight: 20.0000 chunk 26 optimal weight: 20.0000 chunk 28 optimal weight: 4.9990 chunk 27 optimal weight: 30.0000 chunk 15 optimal weight: 20.0000 chunk 25 optimal weight: 7.9990 chunk 5 optimal weight: 20.0000 chunk 8 optimal weight: 5.9990 overall best weight: 5.7788 ------------------------------------------------------------------------------- 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 = 0.4727 r_free = 0.4727 target = 0.102663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.084676 restraints weight = 7105.600| |-----------------------------------------------------------------------------| r_work (start): 0.4465 rms_B_bonded: 3.75 r_work: 0.4362 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.4362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2274 Z= 0.263 Angle : 0.549 5.115 3066 Z= 0.299 Chirality : 0.052 0.141 402 Planarity : 0.002 0.008 384 Dihedral : 5.748 17.627 324 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 4.82 % Allowed : 11.40 % 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: -3.45 (0.37), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.62 (0.28), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 50 PHE 0.012 0.003 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 13 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 2 time to evaluate : 0.258 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 13 average time/residue: 1.4630 time to fit residues: 19.6658 Evaluate side-chains 6 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 1 time to evaluate : 0.256 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 11 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 chunk 2 optimal weight: 20.0000 chunk 9 optimal weight: 30.0000 chunk 22 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 13 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 20 optimal weight: 50.0000 chunk 26 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 79 GLN C 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.102866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.085486 restraints weight = 7161.336| |-----------------------------------------------------------------------------| r_work (start): 0.4433 rms_B_bonded: 3.56 r_work: 0.4308 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.4308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2274 Z= 0.220 Angle : 0.488 5.091 3066 Z= 0.266 Chirality : 0.051 0.139 402 Planarity : 0.002 0.006 384 Dihedral : 5.534 16.463 324 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 1.75 % Allowed : 14.04 % 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: -3.46 (0.38), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.63 (0.29), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 50 PHE 0.011 0.002 PHE E 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 to be fit. rotamer outliers: 4 poor density : 2 time to evaluate : 0.276 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 6 average time/residue: 1.3122 time to fit residues: 8.4059 Evaluate side-chains 4 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1 time to evaluate : 0.236 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 10.0000 chunk 14 optimal weight: 30.0000 chunk 9 optimal weight: 40.0000 chunk 0 optimal weight: 50.0000 chunk 8 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 chunk 11 optimal weight: 7.9990 chunk 10 optimal weight: 30.0000 chunk 4 optimal weight: 10.0000 overall best weight: 8.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.099774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.082448 restraints weight = 7361.455| |-----------------------------------------------------------------------------| r_work (start): 0.4373 rms_B_bonded: 3.50 r_work: 0.4254 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.4254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 2274 Z= 0.385 Angle : 0.599 5.895 3066 Z= 0.327 Chirality : 0.052 0.139 402 Planarity : 0.002 0.016 384 Dihedral : 6.172 21.517 324 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 3.07 % Allowed : 12.28 % 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: -3.65 (0.37), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.77 (0.29), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 PHE 0.014 0.003 PHE A 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 7 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 0 time to evaluate : 0.236 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 7 average time/residue: 0.5283 time to fit residues: 4.2340 Evaluate side-chains 5 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 0 time to evaluate : 0.256 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 20.0000 chunk 29 optimal weight: 30.0000 chunk 13 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 10 optimal weight: 50.0000 chunk 6 optimal weight: 4.9990 chunk 21 optimal weight: 20.0000 chunk 7 optimal weight: 7.9990 chunk 11 optimal weight: 0.0980 chunk 26 optimal weight: 8.9990 chunk 23 optimal weight: 6.9990 overall best weight: 5.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4744 r_free = 0.4744 target = 0.103589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.087116 restraints weight = 7293.279| |-----------------------------------------------------------------------------| r_work (start): 0.4532 rms_B_bonded: 3.51 r_work: 0.4391 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.4391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.4025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 2274 Z= 0.238 Angle : 0.495 5.537 3066 Z= 0.270 Chirality : 0.051 0.140 402 Planarity : 0.002 0.015 384 Dihedral : 5.591 18.416 324 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 2.63 % Allowed : 12.28 % Favored : 85.09 % 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: -3.59 (0.38), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.73 (0.29), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 50 PHE 0.012 0.003 PHE E 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 6 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 0 time to evaluate : 0.250 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 6 average time/residue: 0.4176 time to fit residues: 3.0026 Evaluate side-chains 5 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 0 time to evaluate : 0.250 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 18 optimal weight: 4.9990 chunk 17 optimal weight: 20.0000 chunk 14 optimal weight: 30.0000 chunk 2 optimal weight: 20.0000 chunk 7 optimal weight: 10.0000 chunk 21 optimal weight: 20.0000 chunk 10 optimal weight: 50.0000 chunk 4 optimal weight: 20.0000 chunk 16 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 overall best weight: 6.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4726 r_free = 0.4726 target = 0.102251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.085532 restraints weight = 7378.892| |-----------------------------------------------------------------------------| r_work (start): 0.4500 rms_B_bonded: 3.54 r_work: 0.4370 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.4370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.4179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2274 Z= 0.289 Angle : 0.523 5.847 3066 Z= 0.285 Chirality : 0.051 0.140 402 Planarity : 0.002 0.010 384 Dihedral : 5.758 20.471 324 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 3.07 % Allowed : 12.72 % 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: -3.57 (0.38), 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 0.000 HIS C 50 PHE 0.013 0.003 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 7 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 0 time to evaluate : 0.264 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 7 average time/residue: 0.3579 time to fit residues: 3.0197 Evaluate side-chains 5 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 0 time to evaluate : 0.257 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 6 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 10 optimal weight: 50.0000 chunk 26 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 13 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 2 optimal weight: 8.9990 chunk 8 optimal weight: 8.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4691 r_free = 0.4691 target = 0.100134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.083243 restraints weight = 7759.519| |-----------------------------------------------------------------------------| r_work (start): 0.4422 rms_B_bonded: 3.59 r_work: 0.4298 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.4298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.4400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 2274 Z= 0.351 Angle : 0.569 6.023 3066 Z= 0.312 Chirality : 0.052 0.140 402 Planarity : 0.002 0.014 384 Dihedral : 6.034 22.345 324 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 3.51 % Allowed : 12.72 % 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: -3.64 (0.37), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.77 (0.28), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS C 50 PHE 0.015 0.003 PHE E 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 10 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 2 time to evaluate : 0.251 Fit side-chains REVERT: A 83 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7602 (pm20) outliers start: 8 outliers final: 6 residues processed: 10 average time/residue: 0.6962 time to fit residues: 7.5345 Evaluate side-chains 7 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 1 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain B residue 72 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 8 optimal weight: 5.9990 chunk 19 optimal weight: 30.0000 chunk 9 optimal weight: 20.0000 chunk 11 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 16 optimal weight: 30.0000 chunk 0 optimal weight: 50.0000 chunk 22 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.101217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.084879 restraints weight = 7449.949| |-----------------------------------------------------------------------------| r_work (start): 0.4446 rms_B_bonded: 3.42 r_work: 0.4321 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.4321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.4540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 2274 Z= 0.279 Angle : 0.518 6.006 3066 Z= 0.282 Chirality : 0.051 0.140 402 Planarity : 0.002 0.010 384 Dihedral : 5.723 21.056 324 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 2.63 % Allowed : 13.16 % 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: -3.65 (0.37), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.78 (0.28), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 50 PHE 0.013 0.003 PHE B 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 7 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 1 time to evaluate : 0.235 Fit side-chains REVERT: A 83 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7576 (pm20) outliers start: 6 outliers final: 5 residues processed: 7 average time/residue: 0.7215 time to fit residues: 5.5706 Evaluate side-chains 6 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 1 time to evaluate : 0.265 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 17 optimal weight: 0.0270 chunk 21 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 19 optimal weight: 30.0000 chunk 1 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 25 optimal weight: 40.0000 chunk 23 optimal weight: 9.9990 chunk 16 optimal weight: 20.0000 overall best weight: 3.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4723 r_free = 0.4723 target = 0.103201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.087343 restraints weight = 7393.043| |-----------------------------------------------------------------------------| r_work (start): 0.4493 rms_B_bonded: 3.37 r_work: 0.4367 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.4367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.4713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2274 Z= 0.152 Angle : 0.443 5.437 3066 Z= 0.241 Chirality : 0.050 0.140 402 Planarity : 0.001 0.008 384 Dihedral : 5.202 17.930 324 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 1.75 % Allowed : 14.04 % 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: -3.51 (0.38), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.67 (0.29), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 50 PHE 0.011 0.002 PHE E 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 4 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 0 time to evaluate : 0.266 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 4 average time/residue: 0.6151 time to fit residues: 2.9151 Evaluate side-chains 2 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 0 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E 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 3 optimal weight: 7.9990 chunk 20 optimal weight: 40.0000 chunk 5 optimal weight: 50.0000 chunk 1 optimal weight: 5.9990 chunk 11 optimal weight: 0.0870 chunk 12 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 22 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 15 optimal weight: 0.0370 overall best weight: 3.2242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4724 r_free = 0.4724 target = 0.103059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.087125 restraints weight = 7484.092| |-----------------------------------------------------------------------------| r_work (start): 0.4493 rms_B_bonded: 3.47 r_work: 0.4369 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.4369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.4788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2274 Z= 0.157 Angle : 0.435 5.467 3066 Z= 0.237 Chirality : 0.050 0.139 402 Planarity : 0.001 0.007 384 Dihedral : 5.082 17.448 324 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % 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: -3.38 (0.38), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.57 (0.29), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 50 PHE 0.010 0.002 PHE E 94 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2083.22 seconds wall clock time: 36 minutes 22.95 seconds (2182.95 seconds total)