Starting phenix.real_space_refine on Fri Aug 22 12:38:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zwh_60527/08_2025/8zwh_60527.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zwh_60527/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8zwh_60527/08_2025/8zwh_60527.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zwh_60527/08_2025/8zwh_60527.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zwh_60527/08_2025/8zwh_60527.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zwh_60527/08_2025/8zwh_60527.map" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2268 Number of models: 1 Model: "" Number of chains: 1 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} Restraints were copied for chains: B, D, A, F, C Time building chain proxies: 0.57, per 1000 atoms: 0.25 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: 0.18 Conformation dependent library (CDL) restraints added in 97.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.10 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: 0.30 Time building geometry restraints manager: 0.25 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: 0.01 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'B' selection = chain 'D' selection = chain 'A' selection = chain 'F' selection = chain 'C' } 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: 1.580 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: 0.050 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.940 Find NCS groups from input model: 0.020 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:8.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.100 ------------------------------------------------------------------------------- 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= 0.475 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 PHE 0.019 0.006 PHE A 94 HIS 0.002 0.001 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.01104 ( 2274) covalent geometry : angle 0.90695 ( 3066) hydrogen bonds : bond 0.18382 ( 31) hydrogen bonds : angle 8.99376 ( 93) *********************** 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 : 0.151 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.9068 time to fit residues: 14.8044 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 : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 24 optimal weight: 8.9990 chunk 28 optimal weight: 8.9990 chunk 13 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 chunk 8 optimal weight: 20.0000 chunk 16 optimal weight: 8.9990 chunk 15 optimal weight: 0.0770 chunk 29 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 overall best weight: 3.2144 ------------------------------------------------------------------------------- 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 = 0.4746 r_free = 0.4746 target = 0.103930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.086398 restraints weight = 7277.407| |-----------------------------------------------------------------------------| r_work (start): 0.4459 rms_B_bonded: 3.78 r_work: 0.4362 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.4362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2621 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= 0.132 Angle : 0.555 4.894 3066 Z= 0.300 Chirality : 0.051 0.138 402 Planarity : 0.002 0.009 384 Dihedral : 5.780 15.264 324 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.22 (0.38), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.44 (0.29), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.002 PHE B 94 HIS 0.003 0.001 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 2274) covalent geometry : angle 0.55463 ( 3066) hydrogen bonds : bond 0.01610 ( 31) hydrogen bonds : angle 5.10168 ( 93) *********************** 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 3 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.095 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.5037 time to fit residues: 1.6838 Evaluate side-chains 3 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 20.0000 chunk 14 optimal weight: 0.9980 chunk 29 optimal weight: 0.0770 chunk 18 optimal weight: 8.9990 chunk 26 optimal weight: 20.0000 chunk 19 optimal weight: 20.0000 chunk 7 optimal weight: 20.0000 chunk 21 optimal weight: 3.9990 chunk 12 optimal weight: 20.0000 chunk 9 optimal weight: 5.9990 chunk 15 optimal weight: 30.0000 overall best weight: 4.0144 ------------------------------------------------------------------------------- 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 = 0.4715 r_free = 0.4715 target = 0.102981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.085594 restraints weight = 7256.849| |-----------------------------------------------------------------------------| r_work (start): 0.4455 rms_B_bonded: 3.71 r_work: 0.4319 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.4319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2928 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= 0.137 Angle : 0.495 4.764 3066 Z= 0.270 Chirality : 0.051 0.139 402 Planarity : 0.002 0.009 384 Dihedral : 5.400 15.332 324 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.63 % Allowed : 13.60 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.23 (0.38), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.46 (0.29), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.002 PHE B 94 HIS 0.001 0.000 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 2274) covalent geometry : angle 0.49462 ( 3066) hydrogen bonds : bond 0.01410 ( 31) hydrogen bonds : angle 4.89834 ( 93) *********************** 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 7 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 1 time to evaluate : 0.112 Fit side-chains outliers start: 6 outliers final: 0 residues processed: 7 average time/residue: 1.1534 time to fit residues: 8.2971 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 : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 9 optimal weight: 40.0000 chunk 11 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 4 optimal weight: 30.0000 chunk 28 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 10 optimal weight: 50.0000 chunk 3 optimal weight: 20.0000 chunk 19 optimal weight: 20.0000 chunk 21 optimal weight: 0.0270 overall best weight: 6.4046 ------------------------------------------------------------------------------- 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 = 0.4701 r_free = 0.4701 target = 0.101953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.084253 restraints weight = 7256.177| |-----------------------------------------------------------------------------| r_work (start): 0.4454 rms_B_bonded: 3.71 r_work: 0.4310 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.4310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 2274 Z= 0.199 Angle : 0.541 5.348 3066 Z= 0.295 Chirality : 0.052 0.140 402 Planarity : 0.002 0.007 384 Dihedral : 5.767 18.433 324 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 3.07 % Allowed : 11.84 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.41 (0.38), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.59 (0.29), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.003 PHE B 94 HIS 0.001 0.000 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00432 ( 2274) covalent geometry : angle 0.54050 ( 3066) hydrogen bonds : bond 0.01404 ( 31) hydrogen bonds : angle 4.82766 ( 93) *********************** 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 9 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 2 time to evaluate : 0.092 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 9 average time/residue: 0.4786 time to fit residues: 4.5365 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 : 0.091 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain C residue 52 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 4 optimal weight: 30.0000 chunk 24 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 15 optimal weight: 8.9990 chunk 28 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 20 optimal weight: 40.0000 chunk 18 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 overall best weight: 4.5988 ------------------------------------------------------------------------------- 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 = 0.4735 r_free = 0.4735 target = 0.104053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.086308 restraints weight = 7175.678| |-----------------------------------------------------------------------------| r_work (start): 0.4443 rms_B_bonded: 3.72 r_work: 0.4316 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.4316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.3746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2274 Z= 0.146 Angle : 0.483 5.072 3066 Z= 0.263 Chirality : 0.051 0.140 402 Planarity : 0.001 0.005 384 Dihedral : 5.426 16.559 324 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.07 % Allowed : 11.84 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.42 (0.39), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.60 (0.29), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.002 PHE B 94 HIS 0.001 0.000 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 2274) covalent geometry : angle 0.48308 ( 3066) hydrogen bonds : bond 0.01176 ( 31) hydrogen bonds : angle 4.45113 ( 93) *********************** 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 : 0.097 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 7 average time/residue: 0.1726 time to fit residues: 1.3953 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 : 0.091 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain C residue 52 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 13 optimal weight: 1.9990 chunk 4 optimal weight: 30.0000 chunk 9 optimal weight: 30.0000 chunk 1 optimal weight: 20.0000 chunk 3 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 27 optimal weight: 30.0000 chunk 14 optimal weight: 7.9990 chunk 23 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 = 0.4742 r_free = 0.4742 target = 0.104574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.087934 restraints weight = 7440.149| |-----------------------------------------------------------------------------| r_work (start): 0.4509 rms_B_bonded: 3.56 r_work: 0.4370 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.4370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 2274 Z= 0.178 Angle : 0.502 5.333 3066 Z= 0.272 Chirality : 0.051 0.140 402 Planarity : 0.002 0.006 384 Dihedral : 5.515 18.125 324 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.50 (0.38), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.66 (0.29), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.002 PHE A 94 HIS 0.001 0.000 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 2274) covalent geometry : angle 0.50154 ( 3066) hydrogen bonds : bond 0.01326 ( 31) hydrogen bonds : angle 4.57040 ( 93) *********************** 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 : 0.089 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 6 average time/residue: 0.2208 time to fit residues: 1.4937 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 : 0.091 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain C residue 52 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 20.0000 chunk 10 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 28 optimal weight: 20.0000 chunk 4 optimal weight: 30.0000 chunk 20 optimal weight: 9.9990 chunk 19 optimal weight: 30.0000 chunk 22 optimal weight: 6.9990 chunk 16 optimal weight: 0.0570 chunk 3 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 overall best weight: 3.0104 ------------------------------------------------------------------------------- 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 = 0.4777 r_free = 0.4777 target = 0.107304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.090939 restraints weight = 7350.517| |-----------------------------------------------------------------------------| r_work (start): 0.4560 rms_B_bonded: 3.55 r_work: 0.4419 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.4419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2274 Z= 0.104 Angle : 0.428 4.972 3066 Z= 0.234 Chirality : 0.050 0.139 402 Planarity : 0.001 0.014 384 Dihedral : 5.046 15.154 324 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.19 % Allowed : 13.60 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.35 (0.39), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.55 (0.30), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.002 PHE D 94 HIS 0.001 0.000 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 2274) covalent geometry : angle 0.42760 ( 3066) hydrogen bonds : bond 0.00963 ( 31) hydrogen bonds : angle 4.13569 ( 93) *********************** 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 5 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 0 time to evaluate : 0.092 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 5 average time/residue: 0.2502 time to fit residues: 1.4149 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 : 0.091 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain C residue 52 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 8 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 5 optimal weight: 40.0000 chunk 17 optimal weight: 0.1980 chunk 25 optimal weight: 0.8980 chunk 15 optimal weight: 7.9990 chunk 2 optimal weight: 0.4980 chunk 14 optimal weight: 30.0000 chunk 18 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 9 optimal weight: 30.0000 overall best weight: 2.7184 ------------------------------------------------------------------------------- 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 = 0.4730 r_free = 0.4730 target = 0.104548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.087743 restraints weight = 6968.670| |-----------------------------------------------------------------------------| r_work (start): 0.4473 rms_B_bonded: 3.47 r_work: 0.4359 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.4359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.4384 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= 0.096 Angle : 0.407 4.858 3066 Z= 0.223 Chirality : 0.050 0.138 402 Planarity : 0.001 0.009 384 Dihedral : 4.819 14.612 324 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 2.19 % Allowed : 13.60 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.20 (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 PHE 0.007 0.001 PHE A 94 HIS 0.001 0.000 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00204 ( 2274) covalent geometry : angle 0.40678 ( 3066) hydrogen bonds : bond 0.00960 ( 31) hydrogen bonds : angle 4.01436 ( 93) *********************** 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 5 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 0 time to evaluate : 0.063 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 5 average time/residue: 0.1720 time to fit residues: 0.9758 Evaluate side-chains 3 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 0 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain C residue 52 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 14 optimal weight: 30.0000 chunk 16 optimal weight: 8.9990 chunk 29 optimal weight: 30.0000 chunk 23 optimal weight: 5.9990 chunk 5 optimal weight: 50.0000 chunk 1 optimal weight: 8.9990 chunk 28 optimal weight: 4.9990 chunk 9 optimal weight: 30.0000 chunk 7 optimal weight: 6.9990 chunk 10 optimal weight: 50.0000 chunk 6 optimal weight: 7.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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 = 0.4732 r_free = 0.4732 target = 0.101970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.084517 restraints weight = 7333.132| |-----------------------------------------------------------------------------| r_work (start): 0.4472 rms_B_bonded: 3.65 r_work: 0.4339 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.4339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.4287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 2274 Z= 0.208 Angle : 0.516 5.614 3066 Z= 0.282 Chirality : 0.051 0.140 402 Planarity : 0.002 0.013 384 Dihedral : 5.534 18.358 324 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 2.19 % Allowed : 13.60 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 PHE 0.011 0.002 PHE A 94 HIS 0.001 0.000 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00452 ( 2274) covalent geometry : angle 0.51639 ( 3066) hydrogen bonds : bond 0.01437 ( 31) hydrogen bonds : angle 4.46208 ( 93) *********************** 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 6 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 1 time to evaluate : 0.053 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 6 average time/residue: 0.2739 time to fit residues: 1.7552 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 : 0.049 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain C 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: 10.0000 chunk 15 optimal weight: 50.0000 chunk 14 optimal weight: 30.0000 chunk 18 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 29 optimal weight: 30.0000 chunk 19 optimal weight: 20.0000 chunk 2 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 8 optimal weight: 6.9990 overall best weight: 7.7992 ------------------------------------------------------------------------------- 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 = 0.4701 r_free = 0.4701 target = 0.101315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.084611 restraints weight = 7676.228| |-----------------------------------------------------------------------------| r_work (start): 0.4444 rms_B_bonded: 3.51 r_work: 0.4326 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.4326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.4512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 2274 Z= 0.229 Angle : 0.540 5.577 3066 Z= 0.296 Chirality : 0.052 0.139 402 Planarity : 0.002 0.010 384 Dihedral : 5.799 21.309 324 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 2.19 % Allowed : 13.60 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.40 (0.38), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.58 (0.29), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.003 PHE A 94 HIS 0.002 0.001 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00499 ( 2274) covalent geometry : angle 0.53979 ( 3066) hydrogen bonds : bond 0.01433 ( 31) hydrogen bonds : angle 4.49127 ( 93) ********************** 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 7 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 2 time to evaluate : 0.052 Fit side-chains REVERT: A 83 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7631 (pm20) outliers start: 5 outliers final: 4 residues processed: 7 average time/residue: 0.3436 time to fit residues: 2.5213 Evaluate side-chains 5 residues out of total 228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 1 time to evaluate : 0.051 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain C residue 52 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 18 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 14 optimal weight: 20.0000 chunk 7 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 19 optimal weight: 20.0000 chunk 27 optimal weight: 20.0000 chunk 29 optimal weight: 20.0000 chunk 11 optimal weight: 8.9990 chunk 9 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 = 0.4706 r_free = 0.4706 target = 0.102060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.085483 restraints weight = 7655.030| |-----------------------------------------------------------------------------| r_work (start): 0.4453 rms_B_bonded: 3.53 r_work: 0.4331 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.4331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.4625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2274 Z= 0.181 Angle : 0.493 5.323 3066 Z= 0.270 Chirality : 0.051 0.139 402 Planarity : 0.002 0.008 384 Dihedral : 5.493 19.017 324 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 2.19 % Allowed : 13.60 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.39 (0.38), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.58 (0.29), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.002 PHE A 94 HIS 0.002 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 2274) covalent geometry : angle 0.49264 ( 3066) hydrogen bonds : bond 0.01285 ( 31) hydrogen bonds : angle 4.30123 ( 93) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1033.47 seconds wall clock time: 18 minutes 49.12 seconds (1129.12 seconds total)