Starting phenix.real_space_refine on Tue Feb 3 14:51:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9g9v_51158/02_2026/9g9v_51158.cif Found real_map, /net/cci-nas-00/data/ceres_data/9g9v_51158/02_2026/9g9v_51158.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9g9v_51158/02_2026/9g9v_51158.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9g9v_51158/02_2026/9g9v_51158.map" model { file = "/net/cci-nas-00/data/ceres_data/9g9v_51158/02_2026/9g9v_51158.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9g9v_51158/02_2026/9g9v_51158.cif" } resolution = 3.32 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= 0.001 sd= 0.032 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: 5 Type Number sf(0) Gaussians K 5 8.98 5 S 32 5.16 5 C 2692 2.51 5 N 652 2.21 5 O 692 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s 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: 4073 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 1964 Classifications: {'peptide': 261} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 4, 'TRANS': 256} Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 12, 'ASP:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 75 Chain: "B" Number of atoms: 1964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 1964 Classifications: {'peptide': 261} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 4, 'TRANS': 256} Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 12, 'ASP:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 75 Chain: "A" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 75 Unusual residues: {' K': 5, 'Y01': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'Y01': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.18, per 1000 atoms: 0.29 Number of scatterers: 4073 At special positions: 0 Unit cell: (62.4, 79.04, 96.512, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 5 19.00 S 32 16.00 O 692 8.00 N 652 7.00 C 2692 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: 0.34 Conformation dependent library (CDL) restraints added in 97.1 milliseconds 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 968 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 0 sheets defined 86.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'A' and resid 1 through 52 removed outlier: 4.361A pdb=" N ASN A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL A 25 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ASP A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N HIS A 33 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU A 39 " --> pdb=" O MET A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 74 Proline residue: A 71 - end of helix removed outlier: 4.169A pdb=" N ALA A 74 " --> pdb=" O GLU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 92 Processing helix chain 'A' and resid 103 through 147 removed outlier: 3.667A pdb=" N LEU A 116 " --> pdb=" O PHE A 112 " (cutoff:3.500A) Proline residue: A 119 - end of helix Processing helix chain 'A' and resid 155 through 183 removed outlier: 3.813A pdb=" N GLN A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N CYS A 181 " --> pdb=" O ALA A 177 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 198 Processing helix chain 'A' and resid 212 through 217 Processing helix chain 'A' and resid 217 through 243 removed outlier: 3.569A pdb=" N THR A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 260 removed outlier: 3.881A pdb=" N LEU A 247 " --> pdb=" O VAL A 243 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ASN A 250 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N SER A 251 " --> pdb=" O LEU A 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 52 removed outlier: 3.563A pdb=" N VAL B 25 " --> pdb=" O VAL B 21 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ASP B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N HIS B 33 " --> pdb=" O LEU B 29 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU B 39 " --> pdb=" O MET B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 74 Proline residue: B 71 - end of helix removed outlier: 4.169A pdb=" N ALA B 74 " --> pdb=" O GLU B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 92 Processing helix chain 'B' and resid 103 through 147 removed outlier: 3.667A pdb=" N LEU B 116 " --> pdb=" O PHE B 112 " (cutoff:3.500A) Proline residue: B 119 - end of helix Processing helix chain 'B' and resid 155 through 183 removed outlier: 3.813A pdb=" N GLN B 180 " --> pdb=" O ALA B 176 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N CYS B 181 " --> pdb=" O ALA B 177 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU B 183 " --> pdb=" O SER B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 198 Processing helix chain 'B' and resid 212 through 217 Processing helix chain 'B' and resid 217 through 243 removed outlier: 3.569A pdb=" N THR B 233 " --> pdb=" O LEU B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 260 removed outlier: 3.881A pdb=" N LEU B 247 " --> pdb=" O VAL B 243 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR B 248 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ASN B 250 " --> pdb=" O PHE B 246 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N SER B 251 " --> pdb=" O LEU B 247 " (cutoff:3.500A) 336 hydrogen bonds defined for protein. 1008 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: 0.42 Time building geometry restraints manager: 0.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 622 1.32 - 1.44: 1160 1.44 - 1.56: 2336 1.56 - 1.68: 0 1.68 - 1.80: 50 Bond restraints: 4168 Sorted by residual: bond pdb=" CG1 ILE B 118 " pdb=" CD1 ILE B 118 " ideal model delta sigma weight residual 1.513 1.443 0.070 3.90e-02 6.57e+02 3.20e+00 bond pdb=" CG1 ILE A 118 " pdb=" CD1 ILE A 118 " ideal model delta sigma weight residual 1.513 1.443 0.070 3.90e-02 6.57e+02 3.20e+00 bond pdb=" CB THR A 198 " pdb=" CG2 THR A 198 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.48e+00 bond pdb=" CB THR B 198 " pdb=" CG2 THR B 198 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.48e+00 bond pdb=" CG1 ILE B 94 " pdb=" CD1 ILE B 94 " ideal model delta sigma weight residual 1.513 1.465 0.048 3.90e-02 6.57e+02 1.52e+00 ... (remaining 4163 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 5073 1.10 - 2.20: 499 2.20 - 3.30: 62 3.30 - 4.40: 28 4.40 - 5.50: 12 Bond angle restraints: 5674 Sorted by residual: angle pdb=" C LEU A 29 " pdb=" N GLU A 30 " pdb=" CA GLU A 30 " ideal model delta sigma weight residual 120.23 115.27 4.96 1.67e+00 3.59e-01 8.84e+00 angle pdb=" C LEU B 29 " pdb=" N GLU B 30 " pdb=" CA GLU B 30 " ideal model delta sigma weight residual 120.23 115.27 4.96 1.67e+00 3.59e-01 8.84e+00 angle pdb=" N GLU B 30 " pdb=" CA GLU B 30 " pdb=" C GLU B 30 " ideal model delta sigma weight residual 112.99 117.64 -4.65 1.61e+00 3.86e-01 8.35e+00 angle pdb=" N GLU A 30 " pdb=" CA GLU A 30 " pdb=" C GLU A 30 " ideal model delta sigma weight residual 112.99 117.64 -4.65 1.61e+00 3.86e-01 8.35e+00 angle pdb=" CA GLN B 209 " pdb=" C GLN B 209 " pdb=" N THR B 210 " ideal model delta sigma weight residual 114.76 117.65 -2.89 1.14e+00 7.69e-01 6.41e+00 ... (remaining 5669 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.06: 2416 15.06 - 30.12: 134 30.12 - 45.18: 36 45.18 - 60.24: 12 60.24 - 75.30: 4 Dihedral angle restraints: 2602 sinusoidal: 1088 harmonic: 1514 Sorted by residual: dihedral pdb=" CA LYS B 79 " pdb=" C LYS B 79 " pdb=" N PHE B 80 " pdb=" CA PHE B 80 " ideal model delta harmonic sigma weight residual -180.00 -160.43 -19.57 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA LYS A 79 " pdb=" C LYS A 79 " pdb=" N PHE A 80 " pdb=" CA PHE A 80 " ideal model delta harmonic sigma weight residual 180.00 -160.43 -19.57 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA VAL B 243 " pdb=" C VAL B 243 " pdb=" N LEU B 244 " pdb=" CA LEU B 244 " ideal model delta harmonic sigma weight residual 180.00 -163.03 -16.97 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 2599 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.037: 356 0.037 - 0.073: 205 0.073 - 0.109: 85 0.109 - 0.145: 10 0.145 - 0.181: 8 Chirality restraints: 664 Sorted by residual: chirality pdb=" CA GLU A 30 " pdb=" N GLU A 30 " pdb=" C GLU A 30 " pdb=" CB GLU A 30 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.17e-01 chirality pdb=" CA GLU B 30 " pdb=" N GLU B 30 " pdb=" C GLU B 30 " pdb=" CB GLU B 30 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.17e-01 chirality pdb=" CA THR A 93 " pdb=" N THR A 93 " pdb=" C THR A 93 " pdb=" CB THR A 93 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.16 2.00e-01 2.50e+01 6.06e-01 ... (remaining 661 not shown) Planarity restraints: 684 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 24 " -0.012 2.00e-02 2.50e+03 2.35e-02 5.52e+00 pdb=" C ALA B 24 " 0.041 2.00e-02 2.50e+03 pdb=" O ALA B 24 " -0.015 2.00e-02 2.50e+03 pdb=" N VAL B 25 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 24 " 0.012 2.00e-02 2.50e+03 2.35e-02 5.52e+00 pdb=" C ALA A 24 " -0.041 2.00e-02 2.50e+03 pdb=" O ALA A 24 " 0.015 2.00e-02 2.50e+03 pdb=" N VAL A 25 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 85 " 0.010 2.00e-02 2.50e+03 1.43e-02 4.07e+00 pdb=" CG TYR A 85 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR A 85 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR A 85 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 85 " -0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR A 85 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 85 " -0.017 2.00e-02 2.50e+03 pdb=" OH TYR A 85 " 0.021 2.00e-02 2.50e+03 ... (remaining 681 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.82: 1118 2.82 - 3.40: 4864 3.40 - 3.98: 7465 3.98 - 4.56: 10505 4.56 - 5.14: 15075 Nonbonded interactions: 39027 Sorted by model distance: nonbonded pdb=" OD1 ASP A 27 " pdb=" OG SER B 83 " model vdw 2.245 3.040 nonbonded pdb=" OG SER A 83 " pdb=" OD1 ASP B 27 " model vdw 2.245 3.040 nonbonded pdb=" O THR B 198 " pdb=" OG1 THR B 199 " model vdw 2.439 3.040 nonbonded pdb=" O THR A 198 " pdb=" OG1 THR A 199 " model vdw 2.439 3.040 nonbonded pdb=" O THR A 92 " pdb=" OG1 THR A 93 " model vdw 2.445 3.040 ... (remaining 39022 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' and resid 1 through 302) selection = chain 'B' } 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: 1.610 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.050 Find NCS groups from input model: 0.040 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:0.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 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 : 0.007 0.070 4168 Z= 0.299 Angle : 0.749 5.498 5674 Z= 0.459 Chirality : 0.052 0.181 664 Planarity : 0.005 0.024 684 Dihedral : 11.166 75.301 1634 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.53 % Allowed : 1.05 % Favored : 98.42 % 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: -0.06 (0.34), residues: 518 helix: 0.30 (0.22), residues: 412 sheet: None (None), residues: 0 loop : -0.95 (0.70), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 47 TYR 0.021 0.004 TYR A 85 PHE 0.021 0.002 PHE A 202 TRP 0.009 0.002 TRP A 78 HIS 0.003 0.001 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00724 ( 4168) covalent geometry : angle 0.74907 ( 5674) hydrogen bonds : bond 0.10683 ( 336) hydrogen bonds : angle 5.55159 ( 1008) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 86 time to evaluate : 0.150 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 GLU cc_start: 0.8091 (tp30) cc_final: 0.7834 (tp30) REVERT: A 76 VAL cc_start: 0.8447 (m) cc_final: 0.8062 (p) REVERT: A 168 MET cc_start: 0.6991 (tpp) cc_final: 0.6595 (tpp) REVERT: A 255 ARG cc_start: 0.8117 (ttm170) cc_final: 0.7871 (ttp80) REVERT: B 38 GLU cc_start: 0.8097 (tp30) cc_final: 0.7839 (tp30) REVERT: B 76 VAL cc_start: 0.8444 (m) cc_final: 0.8056 (p) REVERT: B 168 MET cc_start: 0.6996 (tpp) cc_final: 0.6594 (tpp) REVERT: B 255 ARG cc_start: 0.8123 (ttm170) cc_final: 0.7876 (ttp80) outliers start: 2 outliers final: 0 residues processed: 88 average time/residue: 0.1151 time to fit residues: 11.5717 Evaluate side-chains 74 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 50 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3663 r_free = 0.3663 target = 0.148975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.103803 restraints weight = 4849.444| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.66 r_work: 0.2836 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4168 Z= 0.150 Angle : 0.511 5.044 5674 Z= 0.290 Chirality : 0.039 0.164 664 Planarity : 0.003 0.023 684 Dihedral : 6.584 49.482 850 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Rotamer: Outliers : 1.05 % Allowed : 7.89 % Favored : 91.05 % 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: 3.09 (0.37), residues: 518 helix: 2.61 (0.24), residues: 418 sheet: None (None), residues: 0 loop : -0.51 (0.70), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 36 TYR 0.014 0.002 TYR A 138 PHE 0.013 0.001 PHE B 109 TRP 0.013 0.002 TRP B 78 HIS 0.001 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 4168) covalent geometry : angle 0.51079 ( 5674) hydrogen bonds : bond 0.04832 ( 336) hydrogen bonds : angle 3.39125 ( 1008) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 78 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 GLU cc_start: 0.8090 (tp30) cc_final: 0.7830 (tp30) REVERT: A 76 VAL cc_start: 0.8476 (m) cc_final: 0.8158 (p) REVERT: A 141 LYS cc_start: 0.7946 (tttt) cc_final: 0.7473 (tptt) REVERT: B 38 GLU cc_start: 0.8086 (tp30) cc_final: 0.7825 (tp30) REVERT: B 76 VAL cc_start: 0.8480 (m) cc_final: 0.8159 (p) REVERT: B 141 LYS cc_start: 0.7947 (tttt) cc_final: 0.7474 (tptt) outliers start: 4 outliers final: 2 residues processed: 78 average time/residue: 0.1098 time to fit residues: 9.9266 Evaluate side-chains 76 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 74 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain B residue 115 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 49 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 18 optimal weight: 0.4980 chunk 31 optimal weight: 0.4980 chunk 25 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3676 r_free = 0.3676 target = 0.149422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.104228 restraints weight = 4770.980| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.62 r_work: 0.2896 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4168 Z= 0.131 Angle : 0.477 4.984 5674 Z= 0.266 Chirality : 0.038 0.145 664 Planarity : 0.003 0.020 684 Dihedral : 5.963 44.563 850 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 1.58 % Allowed : 7.89 % Favored : 90.53 % 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: 3.75 (0.37), residues: 518 helix: 3.12 (0.24), residues: 418 sheet: None (None), residues: 0 loop : -0.54 (0.68), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 255 TYR 0.012 0.002 TYR A 138 PHE 0.014 0.001 PHE B 109 TRP 0.010 0.002 TRP B 78 HIS 0.001 0.000 HIS A 33 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 4168) covalent geometry : angle 0.47688 ( 5674) hydrogen bonds : bond 0.04307 ( 336) hydrogen bonds : angle 3.13309 ( 1008) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 0.145 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 GLU cc_start: 0.7977 (tp30) cc_final: 0.7732 (tp30) REVERT: A 76 VAL cc_start: 0.8598 (m) cc_final: 0.8310 (p) REVERT: A 141 LYS cc_start: 0.8000 (tttt) cc_final: 0.7572 (tptt) REVERT: B 38 GLU cc_start: 0.7981 (tp30) cc_final: 0.7735 (tp30) REVERT: B 76 VAL cc_start: 0.8600 (m) cc_final: 0.8314 (p) REVERT: B 141 LYS cc_start: 0.8004 (tttt) cc_final: 0.7574 (tptt) outliers start: 6 outliers final: 4 residues processed: 80 average time/residue: 0.1264 time to fit residues: 11.6155 Evaluate side-chains 80 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 249 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 11 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.3641 r_free = 0.3641 target = 0.145880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.099713 restraints weight = 4771.141| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.63 r_work: 0.2794 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4168 Z= 0.174 Angle : 0.522 5.127 5674 Z= 0.288 Chirality : 0.039 0.156 664 Planarity : 0.003 0.021 684 Dihedral : 5.921 49.013 850 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.84 % Allowed : 10.26 % Favored : 87.89 % 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: 3.85 (0.37), residues: 518 helix: 3.18 (0.24), residues: 418 sheet: None (None), residues: 0 loop : -0.43 (0.65), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 255 TYR 0.016 0.002 TYR B 138 PHE 0.014 0.001 PHE A 109 TRP 0.006 0.001 TRP A 78 HIS 0.001 0.000 HIS B 98 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 4168) covalent geometry : angle 0.52223 ( 5674) hydrogen bonds : bond 0.04472 ( 336) hydrogen bonds : angle 3.10090 ( 1008) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLU cc_start: 0.7958 (tp30) cc_final: 0.7706 (tp30) REVERT: A 76 VAL cc_start: 0.8590 (m) cc_final: 0.8314 (p) REVERT: B 38 GLU cc_start: 0.7963 (tp30) cc_final: 0.7712 (tp30) REVERT: B 76 VAL cc_start: 0.8593 (m) cc_final: 0.8319 (p) outliers start: 7 outliers final: 7 residues processed: 77 average time/residue: 0.1170 time to fit residues: 10.4317 Evaluate side-chains 79 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 249 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 7 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 14 optimal weight: 7.9990 chunk 45 optimal weight: 0.5980 chunk 15 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3647 r_free = 0.3647 target = 0.146465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.099766 restraints weight = 4765.397| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.66 r_work: 0.2822 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4168 Z= 0.137 Angle : 0.507 7.540 5674 Z= 0.270 Chirality : 0.037 0.147 664 Planarity : 0.003 0.019 684 Dihedral : 5.761 53.670 850 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.58 % Allowed : 11.05 % Favored : 87.37 % 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: 4.04 (0.37), residues: 518 helix: 3.31 (0.24), residues: 418 sheet: None (None), residues: 0 loop : -0.39 (0.66), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 255 TYR 0.022 0.002 TYR B 138 PHE 0.014 0.001 PHE B 109 TRP 0.009 0.002 TRP A 78 HIS 0.001 0.000 HIS B 98 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 4168) covalent geometry : angle 0.50671 ( 5674) hydrogen bonds : bond 0.04140 ( 336) hydrogen bonds : angle 2.97503 ( 1008) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.151 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 VAL cc_start: 0.8611 (m) cc_final: 0.8408 (p) REVERT: A 138 TYR cc_start: 0.7770 (t80) cc_final: 0.7274 (t80) REVERT: A 142 ARG cc_start: 0.7297 (ttt-90) cc_final: 0.6598 (ttm-80) REVERT: B 76 VAL cc_start: 0.8613 (m) cc_final: 0.8411 (p) REVERT: B 138 TYR cc_start: 0.7775 (t80) cc_final: 0.7279 (t80) REVERT: B 142 ARG cc_start: 0.7302 (ttt-90) cc_final: 0.6601 (ttm-80) outliers start: 6 outliers final: 6 residues processed: 78 average time/residue: 0.1176 time to fit residues: 10.6923 Evaluate side-chains 80 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 249 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 11 optimal weight: 0.6980 chunk 40 optimal weight: 6.9990 chunk 15 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 29 optimal weight: 0.0770 chunk 3 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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 = 0.3692 r_free = 0.3692 target = 0.147908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.101212 restraints weight = 4881.357| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.62 r_work: 0.2902 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4168 Z= 0.119 Angle : 0.485 5.766 5674 Z= 0.260 Chirality : 0.036 0.139 664 Planarity : 0.003 0.020 684 Dihedral : 5.709 59.548 850 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.58 % Allowed : 9.47 % Favored : 88.95 % 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: 4.17 (0.37), residues: 518 helix: 3.43 (0.24), residues: 418 sheet: None (None), residues: 0 loop : -0.47 (0.65), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 255 TYR 0.016 0.002 TYR A 138 PHE 0.018 0.001 PHE B 109 TRP 0.009 0.001 TRP A 78 HIS 0.001 0.000 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 4168) covalent geometry : angle 0.48521 ( 5674) hydrogen bonds : bond 0.03892 ( 336) hydrogen bonds : angle 2.87167 ( 1008) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 0.146 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 VAL cc_start: 0.8758 (m) cc_final: 0.8524 (p) REVERT: A 138 TYR cc_start: 0.7843 (t80) cc_final: 0.7268 (t80) REVERT: A 142 ARG cc_start: 0.7330 (ttt-90) cc_final: 0.6608 (ttm-80) REVERT: B 76 VAL cc_start: 0.8756 (m) cc_final: 0.8519 (p) REVERT: B 138 TYR cc_start: 0.7851 (t80) cc_final: 0.7267 (t80) REVERT: B 142 ARG cc_start: 0.7335 (ttt-90) cc_final: 0.6612 (ttm-80) outliers start: 6 outliers final: 4 residues processed: 81 average time/residue: 0.1152 time to fit residues: 10.8804 Evaluate side-chains 80 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 249 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 42 optimal weight: 0.9990 chunk 21 optimal weight: 0.4980 chunk 22 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 33 optimal weight: 0.0870 chunk 39 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 11 optimal weight: 0.5980 chunk 5 optimal weight: 7.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- 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 = 0.3715 r_free = 0.3715 target = 0.149389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.102173 restraints weight = 4814.184| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.59 r_work: 0.2920 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4168 Z= 0.121 Angle : 0.504 5.578 5674 Z= 0.271 Chirality : 0.036 0.151 664 Planarity : 0.003 0.022 684 Dihedral : 5.578 56.437 850 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.32 % Allowed : 10.00 % Favored : 88.68 % 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: 4.21 (0.37), residues: 518 helix: 3.47 (0.24), residues: 418 sheet: None (None), residues: 0 loop : -0.52 (0.65), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 255 TYR 0.013 0.001 TYR A 138 PHE 0.020 0.001 PHE B 109 TRP 0.006 0.002 TRP B 78 HIS 0.000 0.000 HIS B 33 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 4168) covalent geometry : angle 0.50353 ( 5674) hydrogen bonds : bond 0.03880 ( 336) hydrogen bonds : angle 2.92137 ( 1008) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 77 time to evaluate : 0.168 Fit side-chains REVERT: A 138 TYR cc_start: 0.7775 (t80) cc_final: 0.7202 (t80) REVERT: A 142 ARG cc_start: 0.7337 (ttt-90) cc_final: 0.6620 (ttm-80) REVERT: B 138 TYR cc_start: 0.7785 (t80) cc_final: 0.7207 (t80) REVERT: B 142 ARG cc_start: 0.7343 (ttt-90) cc_final: 0.6626 (ttm-80) outliers start: 5 outliers final: 5 residues processed: 78 average time/residue: 0.1198 time to fit residues: 10.8815 Evaluate side-chains 77 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 249 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 36 optimal weight: 2.9990 chunk 15 optimal weight: 8.9990 chunk 7 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 30 optimal weight: 7.9990 chunk 12 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3689 r_free = 0.3689 target = 0.146891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.100350 restraints weight = 4794.691| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.55 r_work: 0.2895 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4168 Z= 0.146 Angle : 0.524 5.242 5674 Z= 0.282 Chirality : 0.037 0.168 664 Planarity : 0.003 0.023 684 Dihedral : 5.531 52.614 850 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.32 % Allowed : 10.79 % Favored : 87.89 % 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: 4.16 (0.37), residues: 518 helix: 3.42 (0.24), residues: 418 sheet: None (None), residues: 0 loop : -0.42 (0.65), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 255 TYR 0.012 0.001 TYR A 138 PHE 0.020 0.001 PHE B 109 TRP 0.006 0.002 TRP A 78 HIS 0.001 0.000 HIS B 98 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 4168) covalent geometry : angle 0.52384 ( 5674) hydrogen bonds : bond 0.04048 ( 336) hydrogen bonds : angle 2.95855 ( 1008) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.100 Fit side-chains REVERT: A 138 TYR cc_start: 0.7774 (t80) cc_final: 0.7249 (t80) REVERT: A 142 ARG cc_start: 0.7320 (ttt-90) cc_final: 0.6623 (ttm-80) REVERT: B 138 TYR cc_start: 0.7780 (t80) cc_final: 0.7247 (t80) REVERT: B 142 ARG cc_start: 0.7322 (ttt-90) cc_final: 0.6625 (ttm-80) outliers start: 5 outliers final: 5 residues processed: 75 average time/residue: 0.1039 time to fit residues: 9.0168 Evaluate side-chains 79 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 249 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 35 optimal weight: 0.1980 chunk 13 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3695 r_free = 0.3695 target = 0.147489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.100730 restraints weight = 4884.703| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.58 r_work: 0.2896 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4168 Z= 0.140 Angle : 0.523 5.543 5674 Z= 0.282 Chirality : 0.037 0.166 664 Planarity : 0.003 0.024 684 Dihedral : 5.416 48.479 850 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.32 % Allowed : 11.84 % Favored : 86.84 % 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: 4.08 (0.37), residues: 518 helix: 3.39 (0.24), residues: 418 sheet: None (None), residues: 0 loop : -0.64 (0.64), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 255 TYR 0.012 0.001 TYR A 138 PHE 0.020 0.001 PHE B 109 TRP 0.006 0.002 TRP B 78 HIS 0.001 0.000 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 4168) covalent geometry : angle 0.52326 ( 5674) hydrogen bonds : bond 0.03985 ( 336) hydrogen bonds : angle 2.94369 ( 1008) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.090 Fit side-chains REVERT: A 138 TYR cc_start: 0.7754 (t80) cc_final: 0.7278 (t80) REVERT: A 142 ARG cc_start: 0.7184 (ttt-90) cc_final: 0.6536 (ttm-80) REVERT: B 138 TYR cc_start: 0.7756 (t80) cc_final: 0.7277 (t80) REVERT: B 142 ARG cc_start: 0.7184 (ttt-90) cc_final: 0.6534 (ttm-80) outliers start: 5 outliers final: 5 residues processed: 77 average time/residue: 0.0785 time to fit residues: 6.9826 Evaluate side-chains 79 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 249 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 17 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3678 r_free = 0.3678 target = 0.145648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.098829 restraints weight = 4871.421| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.56 r_work: 0.2869 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4168 Z= 0.173 Angle : 0.572 5.740 5674 Z= 0.308 Chirality : 0.039 0.175 664 Planarity : 0.003 0.023 684 Dihedral : 5.524 45.731 850 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.32 % Allowed : 12.37 % Favored : 86.32 % 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: 3.87 (0.37), residues: 518 helix: 3.26 (0.24), residues: 418 sheet: None (None), residues: 0 loop : -0.78 (0.63), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 255 TYR 0.012 0.002 TYR A 113 PHE 0.021 0.002 PHE B 109 TRP 0.006 0.002 TRP A 78 HIS 0.001 0.000 HIS B 98 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 4168) covalent geometry : angle 0.57246 ( 5674) hydrogen bonds : bond 0.04225 ( 336) hydrogen bonds : angle 3.05023 ( 1008) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.145 Fit side-chains REVERT: A 138 TYR cc_start: 0.7756 (t80) cc_final: 0.7307 (t80) REVERT: A 141 LYS cc_start: 0.7619 (tppt) cc_final: 0.7391 (tptt) REVERT: A 142 ARG cc_start: 0.7180 (ttt-90) cc_final: 0.6579 (ttm-80) REVERT: B 138 TYR cc_start: 0.7751 (t80) cc_final: 0.7302 (t80) REVERT: B 141 LYS cc_start: 0.7617 (tppt) cc_final: 0.7389 (tptt) REVERT: B 142 ARG cc_start: 0.7174 (ttt-90) cc_final: 0.6573 (ttm-80) outliers start: 5 outliers final: 5 residues processed: 77 average time/residue: 0.0749 time to fit residues: 6.8219 Evaluate side-chains 79 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 249 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 6 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3702 r_free = 0.3702 target = 0.147849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.101277 restraints weight = 4838.717| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.55 r_work: 0.2895 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4168 Z= 0.139 Angle : 0.548 6.070 5674 Z= 0.293 Chirality : 0.037 0.163 664 Planarity : 0.003 0.024 684 Dihedral : 5.402 43.433 850 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.32 % Allowed : 12.37 % Favored : 86.32 % 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: 3.97 (0.37), residues: 518 helix: 3.34 (0.24), residues: 418 sheet: None (None), residues: 0 loop : -0.81 (0.63), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 255 TYR 0.011 0.001 TYR A 138 PHE 0.020 0.001 PHE B 109 TRP 0.006 0.002 TRP B 78 HIS 0.001 0.000 HIS A 33 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 4168) covalent geometry : angle 0.54843 ( 5674) hydrogen bonds : bond 0.03947 ( 336) hydrogen bonds : angle 2.97346 ( 1008) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1087.70 seconds wall clock time: 19 minutes 23.32 seconds (1163.32 seconds total)