Starting phenix.real_space_refine on Tue Feb 3 12:19:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oys_71033/02_2026/9oys_71033.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oys_71033/02_2026/9oys_71033.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9oys_71033/02_2026/9oys_71033.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oys_71033/02_2026/9oys_71033.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9oys_71033/02_2026/9oys_71033.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oys_71033/02_2026/9oys_71033.map" } resolution = 3.06 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 18 5.16 5 C 762 2.51 5 N 210 2.21 5 O 228 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-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 1218 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 207 Classifications: {'peptide': 33} Link IDs: {'TRANS': 32} Chain: "B" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 199 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Restraints were copied for chains: C, E, D, F Time building chain proxies: 0.20, per 1000 atoms: 0.16 Number of scatterers: 1218 At special positions: 0 Unit cell: (58.104, 68.864, 38.736, 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 18 16.00 O 228 8.00 N 210 7.00 C 762 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: 0.10 Conformation dependent library (CDL) restraints added in 50.9 milliseconds 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 312 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 50.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.03 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 61 removed outlier: 6.320A pdb=" N MET A 48 " --> pdb=" O ALA C 49 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N THR C 51 " --> pdb=" O MET A 48 " (cutoff:3.500A) removed outlier: 8.978A pdb=" N THR A 50 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ALA C 53 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 9.123A pdb=" N ALA A 52 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 9.651A pdb=" N VAL C 55 " --> pdb=" O ALA A 52 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLY A 54 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N VAL C 57 " --> pdb=" O GLY A 54 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ALA A 56 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N LEU C 59 " --> pdb=" O ALA A 56 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLY A 58 " --> pdb=" O LEU C 59 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N VAL C 61 " --> pdb=" O GLY A 58 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ALA A 60 " --> pdb=" O VAL C 61 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N MET C 48 " --> pdb=" O ALA E 49 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N THR E 51 " --> pdb=" O MET C 48 " (cutoff:3.500A) removed outlier: 9.020A pdb=" N THR C 50 " --> pdb=" O THR E 51 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ALA E 53 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 9.015A pdb=" N ALA C 52 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 9.532A pdb=" N VAL E 55 " --> pdb=" O ALA C 52 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLY C 54 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N VAL E 57 " --> pdb=" O GLY C 54 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ALA C 56 " --> pdb=" O VAL E 57 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N LEU E 59 " --> pdb=" O ALA C 56 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLY C 58 " --> pdb=" O LEU E 59 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N VAL E 61 " --> pdb=" O GLY C 58 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ALA C 60 " --> pdb=" O VAL E 61 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 64 through 65 Processing sheet with id=AA3, first strand: chain 'A' and resid 69 through 73 removed outlier: 6.945A pdb=" N THR C 70 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLY A 71 " --> pdb=" O THR C 70 " (cutoff:3.500A) removed outlier: 8.993A pdb=" N LEU C 69 " --> pdb=" O THR E 70 " (cutoff:3.500A) removed outlier: 9.708A pdb=" N ALA E 72 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N GLY C 71 " --> pdb=" O ALA E 72 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 46 through 53 removed outlier: 6.359A pdb=" N ALA D 46 " --> pdb=" O GLN F 47 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ALA F 49 " --> pdb=" O ALA D 46 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N MET D 48 " --> pdb=" O ALA F 49 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N THR F 51 " --> pdb=" O MET D 48 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N THR D 50 " --> pdb=" O THR F 51 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N ALA F 53 " --> pdb=" O THR D 50 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ALA D 52 " --> pdb=" O ALA F 53 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 56 through 57 Processing sheet with id=AA6, first strand: chain 'B' and resid 64 through 70 removed outlier: 6.572A pdb=" N MET B 65 " --> pdb=" O GLY D 66 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ALA D 68 " --> pdb=" O MET B 65 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N SER B 67 " --> pdb=" O ALA D 68 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N THR D 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU B 69 " --> pdb=" O THR D 70 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N MET D 65 " --> pdb=" O GLY F 66 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N ALA F 68 " --> pdb=" O MET D 65 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N SER D 67 " --> pdb=" O ALA F 68 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N THR F 70 " --> pdb=" O SER D 67 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU D 69 " --> pdb=" O THR F 70 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 13 hydrogen bonds defined for protein. 39 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: 0.11 Time building geometry restraints manager: 0.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 402 1.34 - 1.46: 257 1.46 - 1.57: 529 1.57 - 1.69: 0 1.69 - 1.80: 36 Bond restraints: 1224 Sorted by residual: bond pdb=" CA ALA B 46 " pdb=" C ALA B 46 " ideal model delta sigma weight residual 1.519 1.528 -0.009 1.14e-02 7.69e+03 6.22e-01 bond pdb=" CA ALA F 46 " pdb=" C ALA F 46 " ideal model delta sigma weight residual 1.519 1.528 -0.009 1.14e-02 7.69e+03 6.09e-01 bond pdb=" CA MET E 45 " pdb=" CB MET E 45 " ideal model delta sigma weight residual 1.526 1.540 -0.013 1.76e-02 3.23e+03 5.84e-01 bond pdb=" CA MET C 45 " pdb=" CB MET C 45 " ideal model delta sigma weight residual 1.526 1.540 -0.013 1.76e-02 3.23e+03 5.81e-01 bond pdb=" CA ALA D 46 " pdb=" C ALA D 46 " ideal model delta sigma weight residual 1.519 1.528 -0.009 1.14e-02 7.69e+03 5.77e-01 ... (remaining 1219 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.49: 1339 0.49 - 0.98: 256 0.98 - 1.47: 43 1.47 - 1.96: 6 1.96 - 2.45: 6 Bond angle restraints: 1650 Sorted by residual: angle pdb=" CA MET C 45 " pdb=" CB MET C 45 " pdb=" CG MET C 45 " ideal model delta sigma weight residual 114.10 116.46 -2.36 2.00e+00 2.50e-01 1.40e+00 angle pdb=" CA MET A 45 " pdb=" CB MET A 45 " pdb=" CG MET A 45 " ideal model delta sigma weight residual 114.10 116.45 -2.35 2.00e+00 2.50e-01 1.39e+00 angle pdb=" CA MET E 45 " pdb=" CB MET E 45 " pdb=" CG MET E 45 " ideal model delta sigma weight residual 114.10 116.42 -2.32 2.00e+00 2.50e-01 1.35e+00 angle pdb=" N MET C 65 " pdb=" CA MET C 65 " pdb=" C MET C 65 " ideal model delta sigma weight residual 108.34 109.64 -1.30 1.64e+00 3.72e-01 6.33e-01 angle pdb=" N PHE D 73 " pdb=" CA PHE D 73 " pdb=" CB PHE D 73 " ideal model delta sigma weight residual 112.13 110.94 1.19 1.51e+00 4.39e-01 6.22e-01 ... (remaining 1645 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.54: 582 11.54 - 23.07: 66 23.07 - 34.61: 21 34.61 - 46.14: 9 46.14 - 57.68: 6 Dihedral angle restraints: 684 sinusoidal: 186 harmonic: 498 Sorted by residual: dihedral pdb=" CB MET A 45 " pdb=" CG MET A 45 " pdb=" SD MET A 45 " pdb=" CE MET A 45 " ideal model delta sinusoidal sigma weight residual 180.00 -122.32 -57.68 3 1.50e+01 4.44e-03 9.45e+00 dihedral pdb=" CB MET C 45 " pdb=" CG MET C 45 " pdb=" SD MET C 45 " pdb=" CE MET C 45 " ideal model delta sinusoidal sigma weight residual -180.00 -122.33 -57.67 3 1.50e+01 4.44e-03 9.45e+00 dihedral pdb=" CB MET E 45 " pdb=" CG MET E 45 " pdb=" SD MET E 45 " pdb=" CE MET E 45 " ideal model delta sinusoidal sigma weight residual -180.00 -122.39 -57.61 3 1.50e+01 4.44e-03 9.44e+00 ... (remaining 681 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 115 0.024 - 0.049: 58 0.049 - 0.073: 19 0.073 - 0.097: 3 0.097 - 0.121: 21 Chirality restraints: 216 Sorted by residual: chirality pdb=" CA VAL C 55 " pdb=" N VAL C 55 " pdb=" C VAL C 55 " pdb=" CB VAL C 55 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.66e-01 chirality pdb=" CA VAL A 55 " pdb=" N VAL A 55 " pdb=" C VAL A 55 " pdb=" CB VAL A 55 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.60e-01 chirality pdb=" CA VAL E 55 " pdb=" N VAL E 55 " pdb=" C VAL E 55 " pdb=" CB VAL E 55 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.54e-01 ... (remaining 213 not shown) Planarity restraints: 204 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET C 45 " 0.005 2.00e-02 2.50e+03 1.02e-02 1.04e+00 pdb=" C MET C 45 " -0.018 2.00e-02 2.50e+03 pdb=" O MET C 45 " 0.007 2.00e-02 2.50e+03 pdb=" N ALA C 46 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 45 " 0.005 2.00e-02 2.50e+03 1.00e-02 1.00e+00 pdb=" C MET A 45 " -0.017 2.00e-02 2.50e+03 pdb=" O MET A 45 " 0.007 2.00e-02 2.50e+03 pdb=" N ALA A 46 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET E 45 " 0.005 2.00e-02 2.50e+03 9.86e-03 9.71e-01 pdb=" C MET E 45 " -0.017 2.00e-02 2.50e+03 pdb=" O MET E 45 " 0.006 2.00e-02 2.50e+03 pdb=" N ALA E 46 " 0.006 2.00e-02 2.50e+03 ... (remaining 201 not shown) Histogram of nonbonded interaction distances: 2.61 - 3.07: 750 3.07 - 3.53: 1194 3.53 - 3.98: 1665 3.98 - 4.44: 1993 4.44 - 4.90: 3576 Nonbonded interactions: 9178 Sorted by model distance: nonbonded pdb=" OG1 THR B 51 " pdb=" OG1 THR D 70 " model vdw 2.610 3.040 nonbonded pdb=" O LEU D 59 " pdb=" N ALA F 60 " model vdw 2.614 3.120 nonbonded pdb=" O ALA C 56 " pdb=" N VAL E 57 " model vdw 2.636 3.120 nonbonded pdb=" CB LEU F 44 " pdb=" N MET F 45 " model vdw 2.653 2.816 nonbonded pdb=" O LEU B 59 " pdb=" N ALA D 60 " model vdw 2.653 3.120 ... (remaining 9173 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' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 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: 0.020 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 2.910 Find NCS groups from input model: 0.010 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:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 5.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 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 : 0.002 0.013 1224 Z= 0.104 Angle : 0.410 2.452 1650 Z= 0.228 Chirality : 0.044 0.121 216 Planarity : 0.001 0.010 204 Dihedral : 13.409 57.676 372 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.00 % Allowed : 25.00 % Favored : 75.00 % 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: -2.71 (0.55), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.05 (0.42), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.002 0.000 PHE B 73 HIS 0.002 0.001 HIS A 63 Details of bonding type rmsd covalent geometry : bond 0.00171 ( 1224) covalent geometry : angle 0.41018 ( 1650) hydrogen bonds : bond 0.14264 ( 13) hydrogen bonds : angle 8.25202 ( 39) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.022 Fit side-chains REVERT: E 59 LEU cc_start: 0.8925 (tp) cc_final: 0.8704 (tp) REVERT: D 65 MET cc_start: 0.8306 (mtp) cc_final: 0.7867 (mtm) REVERT: F 45 MET cc_start: 0.7991 (tpt) cc_final: 0.7604 (tpt) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0218 time to fit residues: 0.6814 Evaluate side-chains 25 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 12 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 47 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.120885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.105885 restraints weight = 1212.876| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.77 r_work: 0.3254 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 1224 Z= 0.157 Angle : 0.450 3.673 1650 Z= 0.236 Chirality : 0.046 0.128 216 Planarity : 0.002 0.007 204 Dihedral : 3.642 9.215 186 Min Nonbonded Distance : 2.653 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 4.63 % Allowed : 21.30 % Favored : 74.07 % 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: -2.69 (0.55), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.04 (0.42), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.001 PHE C 73 HIS 0.004 0.001 HIS E 63 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 1224) covalent geometry : angle 0.45000 ( 1650) hydrogen bonds : bond 0.01388 ( 13) hydrogen bonds : angle 5.30208 ( 39) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 0.023 Fit side-chains REVERT: C 65 MET cc_start: 0.7829 (mmm) cc_final: 0.7430 (mmm) REVERT: E 59 LEU cc_start: 0.8903 (tp) cc_final: 0.8596 (tp) REVERT: D 65 MET cc_start: 0.8526 (mtp) cc_final: 0.8011 (mtm) REVERT: D 69 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.7905 (tt) outliers start: 5 outliers final: 2 residues processed: 28 average time/residue: 0.0206 time to fit residues: 0.6997 Evaluate side-chains 27 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 69 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 11 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 5 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 16 optimal weight: 0.3980 chunk 10 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 63 HIS F 47 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.116715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.100902 restraints weight = 1226.731| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.89 r_work: 0.3231 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 1224 Z= 0.148 Angle : 0.433 3.392 1650 Z= 0.230 Chirality : 0.046 0.132 216 Planarity : 0.002 0.007 204 Dihedral : 3.663 8.518 186 Min Nonbonded Distance : 2.656 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.70 % Allowed : 21.30 % Favored : 75.00 % 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: -2.81 (0.54), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.13 (0.41), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.001 PHE E 73 HIS 0.003 0.001 HIS C 63 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 1224) covalent geometry : angle 0.43252 ( 1650) hydrogen bonds : bond 0.01353 ( 13) hydrogen bonds : angle 4.86062 ( 39) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.046 Fit side-chains REVERT: C 65 MET cc_start: 0.7866 (mmm) cc_final: 0.7447 (mmm) REVERT: E 59 LEU cc_start: 0.8875 (tp) cc_final: 0.8576 (tp) REVERT: D 65 MET cc_start: 0.8516 (mtp) cc_final: 0.7998 (mtm) REVERT: D 69 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.7867 (tt) outliers start: 4 outliers final: 3 residues processed: 26 average time/residue: 0.0329 time to fit residues: 1.0405 Evaluate side-chains 27 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain D residue 69 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 14 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.3557 r_free = 0.3557 target = 0.118158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.103142 restraints weight = 1261.244| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.80 r_work: 0.3204 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 1224 Z= 0.197 Angle : 0.467 3.481 1650 Z= 0.248 Chirality : 0.047 0.135 216 Planarity : 0.002 0.006 204 Dihedral : 3.925 9.242 186 Min Nonbonded Distance : 2.660 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 7.41 % Allowed : 19.44 % Favored : 73.15 % 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: -2.95 (0.54), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.24 (0.41), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE C 73 HIS 0.005 0.001 HIS C 63 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 1224) covalent geometry : angle 0.46708 ( 1650) hydrogen bonds : bond 0.01347 ( 13) hydrogen bonds : angle 4.67890 ( 39) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 22 time to evaluate : 0.037 Fit side-chains REVERT: C 65 MET cc_start: 0.7943 (OUTLIER) cc_final: 0.7724 (mmm) REVERT: D 48 MET cc_start: 0.8850 (mtp) cc_final: 0.8523 (mtp) REVERT: D 59 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7452 (mt) REVERT: D 65 MET cc_start: 0.8487 (mtp) cc_final: 0.8159 (mtp) REVERT: D 69 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.7957 (tt) outliers start: 8 outliers final: 4 residues processed: 28 average time/residue: 0.0319 time to fit residues: 1.0914 Evaluate side-chains 29 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 22 time to evaluate : 0.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain C residue 65 MET Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain F residue 59 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 17 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 16 optimal weight: 0.0870 chunk 15 optimal weight: 0.7980 chunk 0 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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 = 0.3550 r_free = 0.3550 target = 0.117353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.101952 restraints weight = 1203.982| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.82 r_work: 0.3236 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 1224 Z= 0.139 Angle : 0.424 3.287 1650 Z= 0.226 Chirality : 0.046 0.132 216 Planarity : 0.002 0.006 204 Dihedral : 3.692 9.041 186 Min Nonbonded Distance : 2.659 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 8.33 % Allowed : 19.44 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.94 (0.54), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.23 (0.41), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.001 PHE E 73 HIS 0.003 0.001 HIS C 63 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 1224) covalent geometry : angle 0.42426 ( 1650) hydrogen bonds : bond 0.01014 ( 13) hydrogen bonds : angle 4.41126 ( 39) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 24 time to evaluate : 0.041 Fit side-chains REVERT: C 65 MET cc_start: 0.7908 (OUTLIER) cc_final: 0.7663 (mmm) REVERT: E 59 LEU cc_start: 0.8837 (tp) cc_final: 0.8530 (tp) REVERT: D 48 MET cc_start: 0.8824 (mtp) cc_final: 0.8491 (mtp) REVERT: D 59 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7482 (mt) REVERT: D 69 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.7891 (tt) REVERT: F 45 MET cc_start: 0.7730 (OUTLIER) cc_final: 0.7072 (tpt) outliers start: 9 outliers final: 4 residues processed: 30 average time/residue: 0.0310 time to fit residues: 1.1330 Evaluate side-chains 32 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 24 time to evaluate : 0.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain C residue 65 MET Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain F residue 45 MET Chi-restraints excluded: chain F residue 59 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 4 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 47 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.113126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.098043 restraints weight = 1225.932| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.78 r_work: 0.3175 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.023 1224 Z= 0.251 Angle : 0.517 3.862 1650 Z= 0.274 Chirality : 0.048 0.139 216 Planarity : 0.002 0.007 204 Dihedral : 4.127 9.892 186 Min Nonbonded Distance : 2.662 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 7.41 % Allowed : 19.44 % Favored : 73.15 % 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: -3.06 (0.54), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.33 (0.41), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.001 PHE E 73 HIS 0.006 0.002 HIS C 63 Details of bonding type rmsd covalent geometry : bond 0.00507 ( 1224) covalent geometry : angle 0.51749 ( 1650) hydrogen bonds : bond 0.01516 ( 13) hydrogen bonds : angle 4.63991 ( 39) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 23 time to evaluate : 0.038 Fit side-chains REVERT: C 65 MET cc_start: 0.7987 (OUTLIER) cc_final: 0.7709 (mmm) REVERT: D 48 MET cc_start: 0.8890 (mtp) cc_final: 0.8574 (mtp) REVERT: D 59 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7526 (mt) REVERT: D 69 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.7978 (tt) outliers start: 8 outliers final: 4 residues processed: 29 average time/residue: 0.0302 time to fit residues: 1.0688 Evaluate side-chains 30 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 23 time to evaluate : 0.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain C residue 65 MET Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain F residue 59 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 7 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 47 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.115498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.100366 restraints weight = 1205.102| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.77 r_work: 0.3210 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 1224 Z= 0.188 Angle : 0.468 3.634 1650 Z= 0.248 Chirality : 0.047 0.135 216 Planarity : 0.002 0.008 204 Dihedral : 3.953 9.628 186 Min Nonbonded Distance : 2.660 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 7.41 % Allowed : 20.37 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.08 (0.53), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.34 (0.41), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE E 73 HIS 0.004 0.001 HIS C 63 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 1224) covalent geometry : angle 0.46838 ( 1650) hydrogen bonds : bond 0.01188 ( 13) hydrogen bonds : angle 4.52263 ( 39) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 24 time to evaluate : 0.025 Fit side-chains REVERT: C 65 MET cc_start: 0.7948 (OUTLIER) cc_final: 0.7674 (mmm) REVERT: E 59 LEU cc_start: 0.8880 (tp) cc_final: 0.8587 (tp) REVERT: D 48 MET cc_start: 0.8869 (mtp) cc_final: 0.8546 (mtp) REVERT: D 59 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7477 (mt) REVERT: D 69 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.7948 (tt) outliers start: 8 outliers final: 5 residues processed: 30 average time/residue: 0.0271 time to fit residues: 0.9962 Evaluate side-chains 32 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 24 time to evaluate : 0.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain C residue 65 MET Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain F residue 59 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 16 optimal weight: 0.0000 chunk 0 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 8 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 47 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.115503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.100124 restraints weight = 1227.052| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.79 r_work: 0.3190 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 1224 Z= 0.215 Angle : 0.492 3.731 1650 Z= 0.262 Chirality : 0.047 0.137 216 Planarity : 0.002 0.010 204 Dihedral : 4.034 9.973 186 Min Nonbonded Distance : 2.662 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 9.26 % Allowed : 18.52 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.13 (0.53), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.38 (0.40), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE E 73 HIS 0.005 0.001 HIS C 63 Details of bonding type rmsd covalent geometry : bond 0.00433 ( 1224) covalent geometry : angle 0.49168 ( 1650) hydrogen bonds : bond 0.01319 ( 13) hydrogen bonds : angle 4.56078 ( 39) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 23 time to evaluate : 0.056 Fit side-chains REVERT: C 65 MET cc_start: 0.7988 (OUTLIER) cc_final: 0.7750 (tpp) REVERT: D 48 MET cc_start: 0.8877 (mtp) cc_final: 0.8551 (mtp) REVERT: D 59 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7512 (mt) REVERT: D 69 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8014 (tt) REVERT: F 45 MET cc_start: 0.7697 (OUTLIER) cc_final: 0.6945 (tpt) outliers start: 10 outliers final: 5 residues processed: 30 average time/residue: 0.0336 time to fit residues: 1.2283 Evaluate side-chains 32 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 23 time to evaluate : 0.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain C residue 65 MET Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain F residue 45 MET Chi-restraints excluded: chain F residue 59 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 0 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 16 optimal weight: 0.0670 chunk 17 optimal weight: 0.5980 chunk 7 optimal weight: 0.0970 chunk 5 optimal weight: 1.9990 overall best weight: 0.7518 ------------------------------------------------------------------------------- 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 = 0.3533 r_free = 0.3533 target = 0.117127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.102540 restraints weight = 1230.601| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.74 r_work: 0.3208 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 1224 Z= 0.156 Angle : 0.455 3.982 1650 Z= 0.240 Chirality : 0.046 0.134 216 Planarity : 0.002 0.010 204 Dihedral : 3.838 10.359 186 Min Nonbonded Distance : 2.660 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 9.26 % Allowed : 18.52 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.12 (0.53), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.37 (0.40), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.001 PHE E 73 HIS 0.004 0.001 HIS C 63 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 1224) covalent geometry : angle 0.45489 ( 1650) hydrogen bonds : bond 0.01042 ( 13) hydrogen bonds : angle 4.41690 ( 39) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 24 time to evaluate : 0.038 Fit side-chains REVERT: C 65 MET cc_start: 0.7956 (OUTLIER) cc_final: 0.7730 (tpp) REVERT: E 59 LEU cc_start: 0.8887 (tp) cc_final: 0.8594 (tp) REVERT: D 48 MET cc_start: 0.8835 (mtp) cc_final: 0.8512 (mtp) REVERT: D 59 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7498 (mt) REVERT: D 69 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8010 (tt) REVERT: F 45 MET cc_start: 0.7743 (OUTLIER) cc_final: 0.6953 (tpt) outliers start: 10 outliers final: 5 residues processed: 30 average time/residue: 0.0264 time to fit residues: 0.9796 Evaluate side-chains 33 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 24 time to evaluate : 0.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain C residue 65 MET Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain F residue 45 MET Chi-restraints excluded: chain F residue 59 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 0.3980 chunk 14 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 6 optimal weight: 0.0010 chunk 3 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 overall best weight: 0.4586 ------------------------------------------------------------------------------- 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 = 0.3568 r_free = 0.3568 target = 0.119260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.104732 restraints weight = 1215.307| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.73 r_work: 0.3254 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 1224 Z= 0.107 Angle : 0.415 3.911 1650 Z= 0.219 Chirality : 0.046 0.130 216 Planarity : 0.001 0.009 204 Dihedral : 3.542 9.964 186 Min Nonbonded Distance : 2.660 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 6.48 % Allowed : 21.30 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.04 (0.54), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.31 (0.41), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.003 0.001 PHE C 73 HIS 0.002 0.001 HIS C 63 Details of bonding type rmsd covalent geometry : bond 0.00213 ( 1224) covalent geometry : angle 0.41494 ( 1650) hydrogen bonds : bond 0.00853 ( 13) hydrogen bonds : angle 4.15229 ( 39) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 26 time to evaluate : 0.041 Fit side-chains REVERT: C 65 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.7680 (mmm) REVERT: E 59 LEU cc_start: 0.8799 (tp) cc_final: 0.8531 (tp) REVERT: D 48 MET cc_start: 0.8788 (mtp) cc_final: 0.8458 (mtp) REVERT: D 59 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7411 (mt) REVERT: D 69 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.7988 (tt) REVERT: F 45 MET cc_start: 0.7678 (OUTLIER) cc_final: 0.6944 (tpt) outliers start: 7 outliers final: 3 residues processed: 29 average time/residue: 0.0354 time to fit residues: 1.2432 Evaluate side-chains 33 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 26 time to evaluate : 0.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 65 MET Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain F residue 45 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 12 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 8 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3502 r_free = 0.3502 target = 0.113552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.098030 restraints weight = 1234.709| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.83 r_work: 0.3187 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 1224 Z= 0.213 Angle : 0.492 3.949 1650 Z= 0.260 Chirality : 0.047 0.137 216 Planarity : 0.002 0.008 204 Dihedral : 3.967 10.828 186 Min Nonbonded Distance : 2.663 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 7.41 % Allowed : 20.37 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.13 (0.53), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.38 (0.41), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE E 73 HIS 0.005 0.001 HIS C 63 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 1224) covalent geometry : angle 0.49244 ( 1650) hydrogen bonds : bond 0.01264 ( 13) hydrogen bonds : angle 4.45423 ( 39) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 500.75 seconds wall clock time: 9 minutes 15.36 seconds (555.36 seconds total)