Starting phenix.real_space_refine on Thu Oct 22 17:39:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oig_70523/10_2026/9oig_70523.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oig_70523/10_2026/9oig_70523.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9oig_70523/10_2026/9oig_70523.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oig_70523/10_2026/9oig_70523.map" model { file = "/net/cci-nas-00/data/ceres_data/9oig_70523/10_2026/9oig_70523.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oig_70523/10_2026/9oig_70523.cif" } resolution = 3.0 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= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 1620 2.51 5 N 475 2.21 5 O 465 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 2580 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 225 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "B" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 256 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "K" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 35 Classifications: {'peptide': 7} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'UNK:plan-1': 7} Unresolved non-hydrogen planarities: 7 Restraints were copied for chains: C, E, G, I, D, F, H, J, L, M, N, O Time building chain proxies: 0.45, per 1000 atoms: 0.17 Number of scatterers: 2580 At special positions: 0 Unit cell: (70.692, 76.446, 37.812, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 465 8.00 N 475 7.00 C 1620 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 5 " - pdb=" SG CYS A 22 " distance=2.03 Simple disulfide: pdb=" SG CYS B 5 " - pdb=" SG CYS B 22 " distance=2.02 Simple disulfide: pdb=" SG CYS C 5 " - pdb=" SG CYS C 22 " distance=2.03 Simple disulfide: pdb=" SG CYS D 5 " - pdb=" SG CYS D 22 " distance=2.02 Simple disulfide: pdb=" SG CYS E 5 " - pdb=" SG CYS E 22 " distance=2.03 Simple disulfide: pdb=" SG CYS F 5 " - pdb=" SG CYS F 22 " distance=2.02 Simple disulfide: pdb=" SG CYS G 5 " - pdb=" SG CYS G 22 " distance=2.03 Simple disulfide: pdb=" SG CYS H 5 " - pdb=" SG CYS H 22 " distance=2.02 Simple disulfide: pdb=" SG CYS I 5 " - pdb=" SG CYS I 22 " distance=2.03 Simple disulfide: pdb=" SG CYS J 5 " - pdb=" SG CYS J 22 " distance=2.02 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: 0.23 Conformation dependent library (CDL) restraints added in 50.0 milliseconds 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 670 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.04 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 4 Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 14 removed outlier: 5.945A pdb=" N GLU A 12 " --> pdb=" O ASN C 13 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N GLU C 12 " --> pdb=" O ASN E 13 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N GLU E 12 " --> pdb=" O ASN G 13 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N GLU G 12 " --> pdb=" O ASN I 13 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 18 through 21 Processing sheet with id=AA4, first strand: chain 'A' and resid 24 through 26 removed outlier: 6.735A pdb=" N VAL C 26 " --> pdb=" O THR A 25 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL E 26 " --> pdb=" O THR C 25 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL G 26 " --> pdb=" O THR E 25 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL I 26 " --> pdb=" O THR G 25 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 11 through 14 removed outlier: 6.559A pdb=" N PHE B 11 " --> pdb=" O GLU D 12 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N LYS D 14 " --> pdb=" O PHE B 11 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ASN B 13 " --> pdb=" O LYS D 14 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N PHE D 11 " --> pdb=" O GLU F 12 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N LYS F 14 " --> pdb=" O PHE D 11 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ASN D 13 " --> pdb=" O LYS F 14 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N PHE F 11 " --> pdb=" O GLU H 12 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N LYS H 14 " --> pdb=" O PHE F 11 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ASN F 13 " --> pdb=" O LYS H 14 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N PHE H 11 " --> pdb=" O GLU J 12 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N LYS J 14 " --> pdb=" O PHE H 11 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ASN H 13 " --> pdb=" O LYS J 14 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 26 through 28 removed outlier: 6.502A pdb=" N VAL B 26 " --> pdb=" O LYS D 27 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL D 26 " --> pdb=" O LYS F 27 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL F 26 " --> pdb=" O LYS H 27 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N VAL H 26 " --> pdb=" O LYS J 27 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 20 hydrogen bonds defined for protein. 60 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: 0.24 Time building geometry restraints manager: 0.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 840 1.34 - 1.46: 561 1.46 - 1.58: 1184 1.58 - 1.70: 0 1.70 - 1.82: 20 Bond restraints: 2605 Sorted by residual: bond pdb=" CG1 ILE I 8 " pdb=" CD1 ILE I 8 " ideal model delta sigma weight residual 1.513 1.417 0.096 3.90e-02 6.57e+02 6.08e+00 bond pdb=" CG1 ILE A 8 " pdb=" CD1 ILE A 8 " ideal model delta sigma weight residual 1.513 1.417 0.096 3.90e-02 6.57e+02 6.02e+00 bond pdb=" CG1 ILE E 8 " pdb=" CD1 ILE E 8 " ideal model delta sigma weight residual 1.513 1.418 0.095 3.90e-02 6.57e+02 5.96e+00 bond pdb=" CG1 ILE G 8 " pdb=" CD1 ILE G 8 " ideal model delta sigma weight residual 1.513 1.418 0.095 3.90e-02 6.57e+02 5.92e+00 bond pdb=" CG1 ILE C 8 " pdb=" CD1 ILE C 8 " ideal model delta sigma weight residual 1.513 1.418 0.095 3.90e-02 6.57e+02 5.89e+00 ... (remaining 2600 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 3087 1.70 - 3.39: 279 3.39 - 5.09: 94 5.09 - 6.79: 10 6.79 - 8.48: 10 Bond angle restraints: 3480 Sorted by residual: angle pdb=" C CYS F 5 " pdb=" N PHE F 6 " pdb=" CA PHE F 6 " ideal model delta sigma weight residual 121.54 130.02 -8.48 1.91e+00 2.74e-01 1.97e+01 angle pdb=" C CYS B 5 " pdb=" N PHE B 6 " pdb=" CA PHE B 6 " ideal model delta sigma weight residual 121.54 129.95 -8.41 1.91e+00 2.74e-01 1.94e+01 angle pdb=" C CYS J 5 " pdb=" N PHE J 6 " pdb=" CA PHE J 6 " ideal model delta sigma weight residual 121.54 129.95 -8.41 1.91e+00 2.74e-01 1.94e+01 angle pdb=" C CYS D 5 " pdb=" N PHE D 6 " pdb=" CA PHE D 6 " ideal model delta sigma weight residual 121.54 129.92 -8.38 1.91e+00 2.74e-01 1.92e+01 angle pdb=" C CYS H 5 " pdb=" N PHE H 6 " pdb=" CA PHE H 6 " ideal model delta sigma weight residual 121.54 129.90 -8.36 1.91e+00 2.74e-01 1.92e+01 ... (remaining 3475 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.65: 1345 11.65 - 23.30: 200 23.30 - 34.95: 50 34.95 - 46.60: 20 46.60 - 58.25: 5 Dihedral angle restraints: 1620 sinusoidal: 630 harmonic: 990 Sorted by residual: dihedral pdb=" CB CYS J 5 " pdb=" SG CYS J 5 " pdb=" SG CYS J 22 " pdb=" CB CYS J 22 " ideal model delta sinusoidal sigma weight residual -86.00 -144.25 58.25 1 1.00e+01 1.00e-02 4.55e+01 dihedral pdb=" CB CYS F 5 " pdb=" SG CYS F 5 " pdb=" SG CYS F 22 " pdb=" CB CYS F 22 " ideal model delta sinusoidal sigma weight residual -86.00 -144.22 58.22 1 1.00e+01 1.00e-02 4.54e+01 dihedral pdb=" CB CYS D 5 " pdb=" SG CYS D 5 " pdb=" SG CYS D 22 " pdb=" CB CYS D 22 " ideal model delta sinusoidal sigma weight residual -86.00 -144.21 58.21 1 1.00e+01 1.00e-02 4.54e+01 ... (remaining 1617 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 315 0.073 - 0.145: 75 0.145 - 0.218: 15 0.218 - 0.290: 0 0.290 - 0.363: 5 Chirality restraints: 410 Sorted by residual: chirality pdb=" CG LEU F 20 " pdb=" CB LEU F 20 " pdb=" CD1 LEU F 20 " pdb=" CD2 LEU F 20 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.29e+00 chirality pdb=" CG LEU D 20 " pdb=" CB LEU D 20 " pdb=" CD1 LEU D 20 " pdb=" CD2 LEU D 20 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.27e+00 chirality pdb=" CG LEU B 20 " pdb=" CB LEU B 20 " pdb=" CD1 LEU B 20 " pdb=" CD2 LEU B 20 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.26e+00 ... (remaining 407 not shown) Planarity restraints: 440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE F 6 " 0.024 2.00e-02 2.50e+03 4.08e-02 2.91e+01 pdb=" CG PHE F 6 " -0.089 2.00e-02 2.50e+03 pdb=" CD1 PHE F 6 " 0.048 2.00e-02 2.50e+03 pdb=" CD2 PHE F 6 " 0.023 2.00e-02 2.50e+03 pdb=" CE1 PHE F 6 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 PHE F 6 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE F 6 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 6 " 0.024 2.00e-02 2.50e+03 4.07e-02 2.90e+01 pdb=" CG PHE H 6 " -0.088 2.00e-02 2.50e+03 pdb=" CD1 PHE H 6 " 0.049 2.00e-02 2.50e+03 pdb=" CD2 PHE H 6 " 0.023 2.00e-02 2.50e+03 pdb=" CE1 PHE H 6 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 PHE H 6 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE H 6 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 6 " 0.024 2.00e-02 2.50e+03 4.07e-02 2.90e+01 pdb=" CG PHE B 6 " -0.088 2.00e-02 2.50e+03 pdb=" CD1 PHE B 6 " 0.048 2.00e-02 2.50e+03 pdb=" CD2 PHE B 6 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 PHE B 6 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 PHE B 6 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE B 6 " 0.001 2.00e-02 2.50e+03 ... (remaining 437 not shown) Histogram of nonbonded interaction distances: 2.65 - 3.10: 1656 3.10 - 3.55: 2538 3.55 - 4.00: 4011 4.00 - 4.45: 4222 4.45 - 4.90: 8665 Nonbonded interactions: 21092 Sorted by model distance: nonbonded pdb=" O PHE A 15 " pdb=" CB PHE A 15 " model vdw 2.648 2.752 nonbonded pdb=" O PHE C 15 " pdb=" CB PHE C 15 " model vdw 2.648 2.752 nonbonded pdb=" O PHE G 15 " pdb=" CB PHE G 15 " model vdw 2.649 2.752 nonbonded pdb=" O PHE I 15 " pdb=" CB PHE I 15 " model vdw 2.649 2.752 nonbonded pdb=" O PHE E 15 " pdb=" CB PHE E 15 " model vdw 2.649 2.752 ... (remaining 21087 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } 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: 0.790 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: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 2.830 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:5.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 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 : 0.006 0.096 2615 Z= 0.300 Angle : 1.240 8.483 3500 Z= 0.715 Chirality : 0.077 0.363 410 Planarity : 0.007 0.041 440 Dihedral : 12.124 43.498 920 Min Nonbonded Distance : 2.648 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 0.00 % Allowed : 15.09 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: -4.67 (0.31), residues: 280 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.55 (0.24), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG J 9 PHE 0.089 0.008 PHE F 6 HIS 0.008 0.003 HIS F 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00649 / 0.30 ( 2605) covalent geometry : angle 1.23300 / 0.71 ( 3480) SS BOND : bond 0.00519 / 0.34 ( 10) SS BOND : angle 2.08901 / 1.43 ( 20) hydrogen bonds : bond 0.19886 / 14.21 ( 20) hydrogen bonds : angle 11.51458 / 7.66 ( 60) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.3733 time to fit residues: 15.8242 Evaluate side-chains 18 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: [12, 24, 13, 1, 8, 16, 15, 9, 11, 18, 6] chunk 12 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 1 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.165450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.141055 restraints weight = 2865.684| |-----------------------------------------------------------------------------| r_work (start): 0.4529 rms_B_bonded: 2.86 r_work: 0.4367 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.4367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2615 Z= 0.161 Angle : 0.673 4.691 3500 Z= 0.373 Chirality : 0.047 0.125 410 Planarity : 0.004 0.055 440 Dihedral : 5.789 20.504 340 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.15 % Allowed : 14.34 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.09 (0.36), residues: 280 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.11 (0.28), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 24 PHE 0.022 0.002 PHE F 6 HIS 0.005 0.002 HIS F 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 ( 2605) covalent geometry : angle 0.66044 / 0.37 ( 3480) SS BOND : bond 0.00270 / 0.17 ( 10) SS BOND : angle 1.85403 / 1.24 ( 20) hydrogen bonds : bond 0.02345 / 1.68 ( 20) hydrogen bonds : angle 4.19698 / 2.89 ( 60) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 16 time to evaluate : 0.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 19 THR cc_start: 0.6781 (OUTLIER) cc_final: 0.6442 (m) REVERT: J 18 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8188 (mt-10) outliers start: 11 outliers final: 5 residues processed: 26 average time/residue: 0.4670 time to fit residues: 12.5179 Evaluate side-chains 20 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 14 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 ASN Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain I residue 19 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: [18, 15, 2, 16, 13, 10, 12, 23, 0, 3, 19] chunk 18 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4637 r_free = 0.4637 target = 0.162434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.137813 restraints weight = 2966.594| |-----------------------------------------------------------------------------| r_work (start): 0.4484 rms_B_bonded: 2.80 r_work: 0.4326 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.4326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2615 Z= 0.148 Angle : 0.639 5.334 3500 Z= 0.351 Chirality : 0.045 0.125 410 Planarity : 0.002 0.024 440 Dihedral : 5.903 21.278 340 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.77 % Allowed : 21.51 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: -4.20 (0.36), residues: 280 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.20 (0.27), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 24 PHE 0.012 0.001 PHE E 6 HIS 0.003 0.001 HIS H 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 ( 2605) covalent geometry : angle 0.62889 / 0.35 ( 3480) SS BOND : bond 0.00492 / 0.30 ( 10) SS BOND : angle 1.63957 / 1.09 ( 20) hydrogen bonds : bond 0.03407 / 2.45 ( 20) hydrogen bonds : angle 3.93222 / 2.70 ( 60) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 13 time to evaluate : 0.057 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 6 PHE cc_start: 0.7570 (m-80) cc_final: 0.7329 (m-80) outliers start: 10 outliers final: 6 residues processed: 22 average time/residue: 0.3321 time to fit residues: 7.6609 Evaluate side-chains 19 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 13 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 ASN Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain I residue 19 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: [12, 0, 21, 10, 20, 13, 16, 6, 11, 19, 7] chunk 12 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 20 optimal weight: 0.4980 chunk 13 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4689 r_free = 0.4689 target = 0.159054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.138235 restraints weight = 3064.498| |-----------------------------------------------------------------------------| r_work (start): 0.4522 rms_B_bonded: 2.58 r_work: 0.4371 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.4371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2615 Z= 0.139 Angle : 0.588 4.697 3500 Z= 0.325 Chirality : 0.044 0.122 410 Planarity : 0.002 0.016 440 Dihedral : 5.740 21.510 340 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 6.42 % Allowed : 21.89 % Favored : 71.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: -4.20 (0.36), residues: 280 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.19 (0.27), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 24 PHE 0.012 0.001 PHE C 6 HIS 0.003 0.001 HIS F 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 ( 2605) covalent geometry : angle 0.57959 / 0.32 ( 3480) SS BOND : bond 0.00419 / 0.27 ( 10) SS BOND : angle 1.45718 / 0.99 ( 20) hydrogen bonds : bond 0.02628 / 1.87 ( 20) hydrogen bonds : angle 3.74181 / 2.60 ( 60) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 13 time to evaluate : 0.102 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 8 residues processed: 28 average time/residue: 0.3356 time to fit residues: 9.8863 Evaluate side-chains 21 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 13 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 ASN Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain I residue 19 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: [13, 21, 15, 6, 8, 22, 2, 11, 10, 19, 0] chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 0.0270 chunk 15 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.157541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.136460 restraints weight = 3047.772| |-----------------------------------------------------------------------------| r_work (start): 0.4523 rms_B_bonded: 2.60 r_work: 0.4375 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.4375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.4346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2615 Z= 0.128 Angle : 0.583 5.192 3500 Z= 0.320 Chirality : 0.044 0.121 410 Planarity : 0.002 0.015 440 Dihedral : 5.588 20.414 340 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.91 % Allowed : 23.40 % Favored : 71.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: -4.15 (0.36), residues: 280 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.16 (0.28), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 24 PHE 0.011 0.001 PHE C 6 HIS 0.003 0.001 HIS H 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 ( 2605) covalent geometry : angle 0.57249 / 0.32 ( 3480) SS BOND : bond 0.00357 / 0.24 ( 10) SS BOND : angle 1.56031 / 1.04 ( 20) hydrogen bonds : bond 0.02336 / 1.68 ( 20) hydrogen bonds : angle 3.49490 / 2.40 ( 60) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 19 time to evaluate : 0.099 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 30 average time/residue: 0.2031 time to fit residues: 6.4787 Evaluate side-chains 26 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 17 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 ASN Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain J residue 19 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: [14, 3, 18, 0, 20, 24, 13, 2, 11, 9, 17] chunk 14 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4612 r_free = 0.4612 target = 0.150516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.130711 restraints weight = 3212.900| |-----------------------------------------------------------------------------| r_work (start): 0.4463 rms_B_bonded: 2.42 r_work: 0.4314 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.4190 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.4190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.4653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 2615 Z= 0.196 Angle : 0.732 13.909 3500 Z= 0.392 Chirality : 0.046 0.124 410 Planarity : 0.002 0.018 440 Dihedral : 6.409 35.458 340 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 5.66 % Allowed : 23.40 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.69 % 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 are not related in a simple way. whole: -4.27 (0.36), residues: 280 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.25 (0.27), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 24 PHE 0.014 0.002 PHE E 6 HIS 0.003 0.001 HIS F 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.20 ( 2605) covalent geometry : angle 0.70444 / 0.38 ( 3480) SS BOND : bond 0.00497 / 0.33 ( 10) SS BOND : angle 2.70317 / 1.30 ( 20) hydrogen bonds : bond 0.02641 / 1.93 ( 20) hydrogen bonds : angle 3.73826 / 2.58 ( 60) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 11 time to evaluate : 0.063 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 10 residues processed: 24 average time/residue: 0.3740 time to fit residues: 9.3420 Evaluate side-chains 21 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 11 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain F residue 4 ASN Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain J residue 19 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: [10, 9, 2, 13, 17, 16, 20, 7, 8, 5, 4] chunk 10 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.151049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.130973 restraints weight = 3160.814| |-----------------------------------------------------------------------------| r_work (start): 0.4478 rms_B_bonded: 2.49 r_work: 0.4328 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.4200 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.4200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.4835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 2615 Z= 0.181 Angle : 0.695 10.417 3500 Z= 0.374 Chirality : 0.046 0.138 410 Planarity : 0.002 0.014 440 Dihedral : 6.229 26.637 340 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 6.04 % Allowed : 23.02 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: -4.30 (0.36), residues: 280 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.27 (0.27), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 24 PHE 0.014 0.002 PHE E 6 HIS 0.003 0.001 HIS F 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.18 ( 2605) covalent geometry : angle 0.67026 / 0.36 ( 3480) SS BOND : bond 0.00475 / 0.31 ( 10) SS BOND : angle 2.54097 / 1.25 ( 20) hydrogen bonds : bond 0.02595 / 1.90 ( 20) hydrogen bonds : angle 3.72760 / 2.58 ( 60) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 14 time to evaluate : 0.099 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 18 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.7986 (mt-10) outliers start: 16 outliers final: 10 residues processed: 27 average time/residue: 0.3752 time to fit residues: 10.5580 Evaluate side-chains 25 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 14 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain J residue 18 GLU Chi-restraints excluded: chain J residue 19 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: [12, 15, 6, 13, 22, 19, 24, 8, 1, 5, 18] chunk 12 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 19 optimal weight: 0.4980 chunk 24 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.153290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.132974 restraints weight = 3194.884| |-----------------------------------------------------------------------------| r_work (start): 0.4502 rms_B_bonded: 2.54 r_work: 0.4352 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.4352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.4880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2615 Z= 0.146 Angle : 0.638 7.732 3500 Z= 0.346 Chirality : 0.045 0.122 410 Planarity : 0.002 0.012 440 Dihedral : 5.953 23.867 340 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 5.28 % Allowed : 24.91 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: -4.34 (0.36), residues: 280 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.30 (0.27), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 24 PHE 0.012 0.001 PHE E 6 HIS 0.003 0.001 HIS F 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 ( 2605) covalent geometry : angle 0.61910 / 0.34 ( 3480) SS BOND : bond 0.00439 / 0.29 ( 10) SS BOND : angle 2.12784 / 1.12 ( 20) hydrogen bonds : bond 0.02265 / 1.65 ( 20) hydrogen bonds : angle 3.54241 / 2.46 ( 60) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 17 time to evaluate : 0.102 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 4 ASN cc_start: 0.7509 (m110) cc_final: 0.6852 (t0) REVERT: D 4 ASN cc_start: 0.7385 (p0) cc_final: 0.6513 (p0) REVERT: J 18 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.7813 (mt-10) outliers start: 14 outliers final: 10 residues processed: 28 average time/residue: 0.2933 time to fit residues: 8.6497 Evaluate side-chains 28 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 17 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain J residue 18 GLU Chi-restraints excluded: chain J residue 19 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: [15, 9, 2, 17, 3, 20, 11, 23, 5, 19, 1] chunk 15 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 1 optimal weight: 0.0010 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 4 ASN ** I 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4687 r_free = 0.4687 target = 0.156202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.135195 restraints weight = 3229.089| |-----------------------------------------------------------------------------| r_work (start): 0.4541 rms_B_bonded: 2.63 r_work: 0.4393 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.4393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.4964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2615 Z= 0.129 Angle : 0.632 8.475 3500 Z= 0.339 Chirality : 0.045 0.124 410 Planarity : 0.002 0.012 440 Dihedral : 5.778 24.724 340 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 4.15 % Allowed : 25.66 % Favored : 70.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: -4.33 (0.36), residues: 280 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.29 (0.28), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 9 PHE 0.011 0.001 PHE C 6 HIS 0.003 0.001 HIS D 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 ( 2605) covalent geometry : angle 0.62009 / 0.33 ( 3480) SS BOND : bond 0.00426 / 0.29 ( 10) SS BOND : angle 1.72739 / 0.98 ( 20) hydrogen bonds : bond 0.02113 / 1.53 ( 20) hydrogen bonds : angle 3.49800 / 2.42 ( 60) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 14 time to evaluate : 0.063 Fit side-chains revert: symmetry clash REVERT: D 4 ASN cc_start: 0.7437 (p0) cc_final: 0.6751 (p0) outliers start: 11 outliers final: 9 residues processed: 23 average time/residue: 0.2937 time to fit residues: 7.1253 Evaluate side-chains 23 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 14 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain J residue 19 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: [19, 17, 9, 3, 18, 7, 22, 5, 12, 2, 21] chunk 19 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 2 optimal weight: 0.3980 chunk 21 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.151401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.130792 restraints weight = 3276.612| |-----------------------------------------------------------------------------| r_work (start): 0.4481 rms_B_bonded: 2.60 r_work: 0.4329 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.4329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.5025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 2615 Z= 0.166 Angle : 0.676 8.959 3500 Z= 0.361 Chirality : 0.046 0.123 410 Planarity : 0.002 0.015 440 Dihedral : 5.963 23.088 340 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 3.40 % Allowed : 26.79 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: -4.39 (0.36), residues: 280 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.34 (0.28), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 24 PHE 0.013 0.001 PHE E 6 HIS 0.003 0.001 HIS D 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.17 ( 2605) covalent geometry : angle 0.66179 / 0.36 ( 3480) SS BOND : bond 0.00510 / 0.34 ( 10) SS BOND : angle 1.91644 / 1.05 ( 20) hydrogen bonds : bond 0.02147 / 1.50 ( 20) hydrogen bonds : angle 3.41989 / 2.40 ( 60) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 11 time to evaluate : 0.115 Fit side-chains revert: symmetry clash REVERT: B 4 ASN cc_start: 0.7019 (m110) cc_final: 0.6725 (t0) REVERT: D 4 ASN cc_start: 0.7424 (p0) cc_final: 0.6543 (p0) outliers start: 9 outliers final: 9 residues processed: 19 average time/residue: 0.2195 time to fit residues: 4.5301 Evaluate side-chains 20 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 11 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain J residue 19 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: [22, 3, 6, 19, 16, 0, 11, 13, 18, 5, 1] chunk 22 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.149241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.128947 restraints weight = 3290.223| |-----------------------------------------------------------------------------| r_work (start): 0.4451 rms_B_bonded: 2.56 r_work: 0.4303 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.4303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.5146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 2615 Z= 0.194 Angle : 0.711 9.009 3500 Z= 0.380 Chirality : 0.047 0.125 410 Planarity : 0.002 0.015 440 Dihedral : 6.193 23.743 340 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer: Outliers : 3.40 % Allowed : 27.17 % Favored : 69.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: -4.42 (0.37), residues: 280 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.36 (0.28), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 24 PHE 0.015 0.002 PHE E 6 HIS 0.003 0.001 HIS F 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.19 ( 2605) covalent geometry : angle 0.69621 / 0.37 ( 3480) SS BOND : bond 0.00554 / 0.37 ( 10) SS BOND : angle 2.00400 / 1.10 ( 20) hydrogen bonds : bond 0.02411 / 1.69 ( 20) hydrogen bonds : angle 3.62831 / 2.55 ( 60) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 922.15 seconds wall clock time: 16 minutes 40.23 seconds (1000.23 seconds total)