Starting phenix.real_space_refine on Wed Jul 1 23:29:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8j1n_35928/07_2026/8j1n_35928.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j1n_35928/07_2026/8j1n_35928.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8j1n_35928/07_2026/8j1n_35928.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j1n_35928/07_2026/8j1n_35928.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8j1n_35928/07_2026/8j1n_35928.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j1n_35928/07_2026/8j1n_35928.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8j1n_35928/07_2026/8j1n_35928.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8j1n_35928/07_2026/8j1n_35928.cif" } resolution = 2.51 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= 0.146 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 P 4 5.49 5 S 18 5.16 5 C 2106 2.51 5 N 545 2.21 5 O 619 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3292 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2180 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 15, 'TRANS': 274} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 997 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "A" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 115 Unusual residues: {'CDL': 1, 'DNF': 1, 'PC1': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 102 Time building chain proxies: 1.15, per 1000 atoms: 0.35 Number of scatterers: 3292 At special positions: 0 Unit cell: (66.72, 68.388, 110.922, 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) S 18 16.00 P 4 15.00 O 619 8.00 N 545 7.00 C 2106 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 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: 0.42 Conformation dependent library (CDL) restraints added in 114.1 milliseconds 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 754 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 3 sheets defined 62.6% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 11 through 43 Proline residue: A 32 - end of helix Processing helix chain 'A' and resid 56 through 69 Processing helix chain 'A' and resid 70 through 73 Processing helix chain 'A' and resid 76 through 107 removed outlier: 4.129A pdb=" N PHE A 101 " --> pdb=" O THR A 97 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LYS A 106 " --> pdb=" O LEU A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 143 removed outlier: 3.512A pdb=" N LYS A 115 " --> pdb=" O SER A 111 " (cutoff:3.500A) Proline residue: A 132 - end of helix Processing helix chain 'A' and resid 155 through 168 Processing helix chain 'A' and resid 169 through 174 removed outlier: 3.603A pdb=" N LYS A 174 " --> pdb=" O GLY A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 205 Processing helix chain 'A' and resid 210 through 242 removed outlier: 3.839A pdb=" N HIS A 214 " --> pdb=" O ASP A 210 " (cutoff:3.500A) Proline residue: A 231 - end of helix Processing helix chain 'A' and resid 249 through 262 Processing helix chain 'A' and resid 263 through 268 removed outlier: 3.655A pdb=" N LYS A 268 " --> pdb=" O ALA A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 297 Processing helix chain 'B' and resid 28 through 32 Processing helix chain 'B' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'B' and resid 11 through 13 removed outlier: 6.727A pdb=" N VAL B 12 " --> pdb=" O SER B 120 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N MET B 34 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ALA B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 11 through 13 removed outlier: 6.727A pdb=" N VAL B 12 " --> pdb=" O SER B 120 " (cutoff:3.500A) 234 hydrogen bonds defined for protein. 648 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: 0.51 Time building geometry restraints manager: 0.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 517 1.30 - 1.43: 891 1.43 - 1.56: 1920 1.56 - 1.69: 8 1.69 - 1.81: 27 Bond restraints: 3363 Sorted by residual: bond pdb=" CA7 CDL A 402 " pdb=" OA8 CDL A 402 " ideal model delta sigma weight residual 1.334 1.457 -0.123 1.10e-02 8.26e+03 1.26e+02 bond pdb=" CB7 CDL A 402 " pdb=" OB8 CDL A 402 " ideal model delta sigma weight residual 1.334 1.442 -0.108 1.10e-02 8.26e+03 9.61e+01 bond pdb=" CA5 CDL A 402 " pdb=" OA6 CDL A 402 " ideal model delta sigma weight residual 1.342 1.458 -0.116 1.50e-02 4.44e+03 5.93e+01 bond pdb=" CB5 CDL A 402 " pdb=" OB6 CDL A 402 " ideal model delta sigma weight residual 1.342 1.445 -0.103 1.50e-02 4.44e+03 4.74e+01 bond pdb=" C21 PC1 A 403 " pdb=" O21 PC1 A 403 " ideal model delta sigma weight residual 1.331 1.457 -0.126 2.00e-02 2.50e+03 3.96e+01 ... (remaining 3358 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 4345 1.95 - 3.90: 144 3.90 - 5.85: 55 5.85 - 7.80: 6 7.80 - 9.75: 9 Bond angle restraints: 4559 Sorted by residual: angle pdb=" C51 CDL A 402 " pdb=" CB5 CDL A 402 " pdb=" OB6 CDL A 402 " ideal model delta sigma weight residual 111.33 120.79 -9.46 1.32e+00 5.72e-01 5.12e+01 angle pdb=" C11 CDL A 402 " pdb=" CA5 CDL A 402 " pdb=" OA6 CDL A 402 " ideal model delta sigma weight residual 111.33 120.58 -9.25 1.32e+00 5.72e-01 4.90e+01 angle pdb=" C71 CDL A 402 " pdb=" CB7 CDL A 402 " pdb=" OB8 CDL A 402 " ideal model delta sigma weight residual 111.64 121.39 -9.75 1.65e+00 3.69e-01 3.51e+01 angle pdb=" C31 CDL A 402 " pdb=" CA7 CDL A 402 " pdb=" OA8 CDL A 402 " ideal model delta sigma weight residual 111.64 120.78 -9.14 1.65e+00 3.69e-01 3.08e+01 angle pdb=" OB6 CDL A 402 " pdb=" CB5 CDL A 402 " pdb=" OB7 CDL A 402 " ideal model delta sigma weight residual 123.92 118.75 5.17 1.00e+00 9.92e-01 2.65e+01 ... (remaining 4554 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 1777 17.56 - 35.12: 141 35.12 - 52.68: 27 52.68 - 70.23: 12 70.23 - 87.79: 4 Dihedral angle restraints: 1961 sinusoidal: 778 harmonic: 1183 Sorted by residual: dihedral pdb=" CA ARG B 72 " pdb=" C ARG B 72 " pdb=" N ASP B 73 " pdb=" CA ASP B 73 " ideal model delta harmonic sigma weight residual 180.00 155.64 24.36 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA TRP B 111 " pdb=" C TRP B 111 " pdb=" N GLY B 112 " pdb=" CA GLY B 112 " ideal model delta harmonic sigma weight residual 180.00 163.83 16.17 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CB GLU A 261 " pdb=" CG GLU A 261 " pdb=" CD GLU A 261 " pdb=" OE1 GLU A 261 " ideal model delta sinusoidal sigma weight residual 0.00 87.79 -87.79 1 3.00e+01 1.11e-03 1.03e+01 ... (remaining 1958 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 337 0.045 - 0.090: 132 0.090 - 0.135: 33 0.135 - 0.180: 3 0.180 - 0.225: 1 Chirality restraints: 506 Sorted by residual: chirality pdb=" CB ILE A 116 " pdb=" CA ILE A 116 " pdb=" CG1 ILE A 116 " pdb=" CG2 ILE A 116 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA VAL A 211 " pdb=" N VAL A 211 " pdb=" C VAL A 211 " pdb=" CB VAL A 211 " both_signs ideal model delta sigma weight residual False 2.44 2.30 0.14 2.00e-01 2.50e+01 5.23e-01 chirality pdb=" CG LEU A 90 " pdb=" CB LEU A 90 " pdb=" CD1 LEU A 90 " pdb=" CD2 LEU A 90 " both_signs ideal model delta sigma weight residual False -2.59 -2.73 0.14 2.00e-01 2.50e+01 4.91e-01 ... (remaining 503 not shown) Planarity restraints: 569 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 101 " 0.025 2.00e-02 2.50e+03 3.82e-02 2.55e+01 pdb=" CG PHE B 101 " -0.086 2.00e-02 2.50e+03 pdb=" CD1 PHE B 101 " 0.039 2.00e-02 2.50e+03 pdb=" CD2 PHE B 101 " 0.024 2.00e-02 2.50e+03 pdb=" CE1 PHE B 101 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE B 101 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE B 101 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 27 " 0.024 5.00e-02 4.00e+02 3.68e-02 2.17e+00 pdb=" N PRO B 28 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 28 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 28 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 96 " -0.007 2.00e-02 2.50e+03 1.35e-02 1.82e+00 pdb=" C ASP A 96 " 0.023 2.00e-02 2.50e+03 pdb=" O ASP A 96 " -0.009 2.00e-02 2.50e+03 pdb=" N THR A 97 " -0.008 2.00e-02 2.50e+03 ... (remaining 566 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 501 2.76 - 3.29: 3101 3.29 - 3.83: 5992 3.83 - 4.36: 6913 4.36 - 4.90: 11952 Nonbonded interactions: 28459 Sorted by model distance: nonbonded pdb=" O TRP A 173 " pdb=" OG1 THR A 176 " model vdw 2.219 3.040 nonbonded pdb=" OG1 THR A 30 " pdb=" NH1 ARG A 276 " model vdw 2.233 3.120 nonbonded pdb=" O GLY A 130 " pdb=" OG1 THR A 133 " model vdw 2.300 3.040 nonbonded pdb=" O ALA A 63 " pdb=" OG1 THR A 67 " model vdw 2.342 3.040 nonbonded pdb=" OE2 GLU B 6 " pdb=" N CYS B 96 " model vdw 2.353 3.120 ... (remaining 28454 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 2.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.180 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 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 : 0.009 0.126 3364 Z= 0.518 Angle : 1.012 9.745 4561 Z= 0.524 Chirality : 0.049 0.225 506 Planarity : 0.005 0.038 569 Dihedral : 14.644 87.792 1204 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.39), residues: 410 helix: 1.87 (0.32), residues: 223 sheet: -0.02 (0.64), residues: 59 loop : 0.60 (0.54), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 70 TYR 0.020 0.002 TYR A 157 PHE 0.086 0.004 PHE B 101 TRP 0.011 0.002 TRP B 56 HIS 0.004 0.001 HIS A 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00947 / 0.52 ( 3363) covalent geometry : angle 1.00980 / 0.52 ( 4559) SS BOND : bond 0.00448 / 0.24 ( 1) SS BOND : angle 2.98172 / 1.74 ( 2) hydrogen bonds : bond 0.09917 / 7.29 ( 230) hydrogen bonds : angle 7.47174 / 5.64 ( 648) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.129 Fit side-chains REVERT: A 157 TYR cc_start: 0.7543 (m-80) cc_final: 0.6787 (t80) REVERT: A 169 LEU cc_start: 0.8127 (mm) cc_final: 0.7893 (mt) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.4267 time to fit residues: 30.4526 Evaluate side-chains 61 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.180798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.132052 restraints weight = 3314.133| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.67 r_work: 0.3339 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3364 Z= 0.154 Angle : 0.565 6.738 4561 Z= 0.294 Chirality : 0.042 0.244 506 Planarity : 0.004 0.036 569 Dihedral : 9.361 58.686 497 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.48 % Allowed : 10.65 % Favored : 87.87 % 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: 2.21 (0.39), residues: 410 helix: 2.51 (0.32), residues: 223 sheet: 0.04 (0.64), residues: 54 loop : 0.34 (0.51), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 161 TYR 0.011 0.001 TYR A 157 PHE 0.031 0.002 PHE B 101 TRP 0.012 0.002 TRP B 111 HIS 0.003 0.001 HIS B 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 3363) covalent geometry : angle 0.56446 / 0.29 ( 4559) SS BOND : bond 0.00199 / 0.10 ( 1) SS BOND : angle 1.49797 / 0.88 ( 2) hydrogen bonds : bond 0.04198 / 2.84 ( 230) hydrogen bonds : angle 5.87328 / 4.42 ( 648) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.122 Fit side-chains REVERT: A 150 LYS cc_start: 0.8358 (tptp) cc_final: 0.8103 (tttm) REVERT: A 157 TYR cc_start: 0.7948 (m-80) cc_final: 0.7069 (t80) REVERT: A 169 LEU cc_start: 0.8409 (mm) cc_final: 0.8101 (mt) REVERT: B 71 SER cc_start: 0.8838 (t) cc_final: 0.8474 (t) REVERT: B 78 THR cc_start: 0.9229 (m) cc_final: 0.8922 (t) REVERT: B 83 MET cc_start: 0.8347 (mtp) cc_final: 0.7966 (mtp) REVERT: B 95 TYR cc_start: 0.8445 (m-80) cc_final: 0.8059 (m-80) REVERT: B 119 VAL cc_start: 0.7800 (OUTLIER) cc_final: 0.7565 (p) outliers start: 5 outliers final: 2 residues processed: 61 average time/residue: 0.4509 time to fit residues: 28.4754 Evaluate side-chains 59 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 119 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 39 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.179429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.129417 restraints weight = 3320.569| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.74 r_work: 0.3319 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 3364 Z= 0.169 Angle : 0.561 6.454 4561 Z= 0.290 Chirality : 0.042 0.197 506 Planarity : 0.004 0.033 569 Dihedral : 9.014 58.320 497 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.07 % Allowed : 12.13 % Favored : 85.80 % 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: 2.45 (0.39), residues: 410 helix: 2.69 (0.32), residues: 223 sheet: 0.36 (0.65), residues: 54 loop : 0.37 (0.52), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 83 TYR 0.014 0.001 TYR A 157 PHE 0.015 0.002 PHE B 101 TRP 0.011 0.002 TRP B 56 HIS 0.004 0.001 HIS B 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 ( 3363) covalent geometry : angle 0.56074 / 0.29 ( 4559) SS BOND : bond 0.00038 / 0.02 ( 1) SS BOND : angle 1.39280 / 0.82 ( 2) hydrogen bonds : bond 0.04093 / 2.76 ( 230) hydrogen bonds : angle 5.66660 / 4.27 ( 648) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.122 Fit side-chains REVERT: A 70 ARG cc_start: 0.7796 (ttm-80) cc_final: 0.7372 (ttp-110) REVERT: A 116 ILE cc_start: 0.7908 (OUTLIER) cc_final: 0.7573 (mp) REVERT: A 150 LYS cc_start: 0.8379 (tptp) cc_final: 0.8108 (tttm) REVERT: A 157 TYR cc_start: 0.7978 (m-80) cc_final: 0.7042 (t80) REVERT: B 71 SER cc_start: 0.8745 (t) cc_final: 0.8444 (t) REVERT: B 83 MET cc_start: 0.8304 (mtp) cc_final: 0.7898 (mtp) REVERT: B 95 TYR cc_start: 0.8472 (m-80) cc_final: 0.8097 (m-80) outliers start: 7 outliers final: 3 residues processed: 53 average time/residue: 0.4756 time to fit residues: 26.0271 Evaluate side-chains 57 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 93 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 24 optimal weight: 0.0040 chunk 11 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 2 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 overall best weight: 1.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.177754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.128089 restraints weight = 3291.359| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.75 r_work: 0.3302 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 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 0.055 3364 Z= 0.190 Angle : 0.572 6.398 4561 Z= 0.294 Chirality : 0.043 0.211 506 Planarity : 0.004 0.034 569 Dihedral : 8.805 56.569 497 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.37 % Allowed : 13.31 % Favored : 84.32 % 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: 2.48 (0.39), residues: 410 helix: 2.70 (0.31), residues: 222 sheet: 0.42 (0.64), residues: 54 loop : 0.42 (0.52), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 276 TYR 0.014 0.001 TYR A 157 PHE 0.013 0.002 PHE A 128 TRP 0.010 0.002 TRP B 56 HIS 0.005 0.001 HIS B 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.19 ( 3363) covalent geometry : angle 0.57163 / 0.29 ( 4559) SS BOND : bond 0.00092 / 0.05 ( 1) SS BOND : angle 1.40563 / 0.82 ( 2) hydrogen bonds : bond 0.04155 / 2.80 ( 230) hydrogen bonds : angle 5.66439 / 4.27 ( 648) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.078 Fit side-chains REVERT: A 150 LYS cc_start: 0.8390 (tptp) cc_final: 0.8112 (tttm) REVERT: A 157 TYR cc_start: 0.8009 (m-80) cc_final: 0.7067 (t80) REVERT: B 71 SER cc_start: 0.8783 (t) cc_final: 0.8482 (t) REVERT: B 95 TYR cc_start: 0.8537 (m-80) cc_final: 0.8150 (m-80) outliers start: 8 outliers final: 4 residues processed: 63 average time/residue: 0.3668 time to fit residues: 23.9470 Evaluate side-chains 60 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 119 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 40 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 29 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.178447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.128708 restraints weight = 3306.170| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.75 r_work: 0.3309 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 3364 Z= 0.167 Angle : 0.542 6.317 4561 Z= 0.278 Chirality : 0.041 0.203 506 Planarity : 0.004 0.034 569 Dihedral : 8.489 55.192 497 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.66 % Allowed : 15.09 % Favored : 82.25 % 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: 2.70 (0.39), residues: 410 helix: 2.89 (0.31), residues: 222 sheet: 0.54 (0.64), residues: 54 loop : 0.49 (0.53), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 39 TYR 0.013 0.001 TYR A 157 PHE 0.012 0.002 PHE A 128 TRP 0.009 0.002 TRP B 56 HIS 0.004 0.001 HIS B 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 ( 3363) covalent geometry : angle 0.54189 / 0.28 ( 4559) SS BOND : bond 0.00022 / 0.01 ( 1) SS BOND : angle 1.17211 / 0.69 ( 2) hydrogen bonds : bond 0.03999 / 2.68 ( 230) hydrogen bonds : angle 5.54533 / 4.19 ( 648) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.122 Fit side-chains REVERT: A 70 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.7261 (ttm-80) REVERT: A 150 LYS cc_start: 0.8380 (tptp) cc_final: 0.8104 (tttm) REVERT: A 157 TYR cc_start: 0.7978 (m-80) cc_final: 0.7044 (t80) REVERT: B 71 SER cc_start: 0.8739 (t) cc_final: 0.8499 (t) REVERT: B 95 TYR cc_start: 0.8566 (m-80) cc_final: 0.8149 (m-80) outliers start: 9 outliers final: 5 residues processed: 61 average time/residue: 0.4012 time to fit residues: 25.4202 Evaluate side-chains 60 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 119 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 2 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.179751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.130280 restraints weight = 3303.474| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.74 r_work: 0.3345 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3364 Z= 0.138 Angle : 0.514 6.216 4561 Z= 0.262 Chirality : 0.040 0.197 506 Planarity : 0.004 0.032 569 Dihedral : 8.176 54.497 497 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.37 % Allowed : 15.68 % Favored : 81.95 % 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: 2.90 (0.39), residues: 410 helix: 3.08 (0.31), residues: 222 sheet: 0.64 (0.64), residues: 54 loop : 0.52 (0.53), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 104 TYR 0.012 0.001 TYR A 157 PHE 0.009 0.001 PHE A 128 TRP 0.008 0.001 TRP B 111 HIS 0.003 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 3363) covalent geometry : angle 0.51356 / 0.26 ( 4559) SS BOND : bond 0.00007 / 0.00 ( 1) SS BOND : angle 1.06872 / 0.63 ( 2) hydrogen bonds : bond 0.03804 / 2.55 ( 230) hydrogen bonds : angle 5.38326 / 4.07 ( 648) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.125 Fit side-chains REVERT: A 70 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.7236 (ttm-80) REVERT: A 150 LYS cc_start: 0.8368 (tptp) cc_final: 0.8110 (tttm) REVERT: A 157 TYR cc_start: 0.7906 (m-80) cc_final: 0.7071 (t80) REVERT: A 169 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8037 (mt) REVERT: B 71 SER cc_start: 0.8719 (t) cc_final: 0.8247 (p) REVERT: B 83 MET cc_start: 0.8327 (mtp) cc_final: 0.8057 (mtp) REVERT: B 95 TYR cc_start: 0.8574 (m-80) cc_final: 0.8238 (m-80) outliers start: 8 outliers final: 4 residues processed: 64 average time/residue: 0.3810 time to fit residues: 25.3764 Evaluate side-chains 63 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 119 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 15 optimal weight: 0.4980 chunk 7 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 39 optimal weight: 0.4980 chunk 8 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.179926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.132051 restraints weight = 3376.951| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.03 r_work: 0.3303 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3364 Z= 0.136 Angle : 0.517 6.261 4561 Z= 0.264 Chirality : 0.040 0.197 506 Planarity : 0.004 0.031 569 Dihedral : 8.033 53.576 497 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.07 % Allowed : 17.16 % Favored : 80.77 % 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: 2.99 (0.39), residues: 410 helix: 3.14 (0.31), residues: 222 sheet: 0.73 (0.64), residues: 54 loop : 0.55 (0.53), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 104 TYR 0.012 0.001 TYR A 157 PHE 0.010 0.001 PHE A 128 TRP 0.008 0.001 TRP B 56 HIS 0.003 0.001 HIS B 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 3363) covalent geometry : angle 0.51717 / 0.26 ( 4559) SS BOND : bond 0.00047 / 0.02 ( 1) SS BOND : angle 0.99227 / 0.58 ( 2) hydrogen bonds : bond 0.03799 / 2.55 ( 230) hydrogen bonds : angle 5.31790 / 4.02 ( 648) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.122 Fit side-chains REVERT: A 70 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.7230 (ttm-80) REVERT: A 150 LYS cc_start: 0.8352 (tptp) cc_final: 0.8103 (tttm) REVERT: A 157 TYR cc_start: 0.7934 (m-80) cc_final: 0.7079 (t80) REVERT: A 169 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8018 (mt) REVERT: B 71 SER cc_start: 0.8681 (t) cc_final: 0.8214 (p) REVERT: B 83 MET cc_start: 0.8266 (mtp) cc_final: 0.7953 (mtp) REVERT: B 95 TYR cc_start: 0.8526 (m-80) cc_final: 0.8084 (m-80) outliers start: 7 outliers final: 3 residues processed: 64 average time/residue: 0.4325 time to fit residues: 28.6911 Evaluate side-chains 64 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 119 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 29 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 25 optimal weight: 0.1980 chunk 35 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.179915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.132073 restraints weight = 3361.128| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.05 r_work: 0.3314 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3364 Z= 0.138 Angle : 0.525 6.358 4561 Z= 0.269 Chirality : 0.041 0.240 506 Planarity : 0.004 0.030 569 Dihedral : 7.990 53.154 497 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.66 % Allowed : 16.86 % Favored : 80.47 % 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: 3.01 (0.39), residues: 410 helix: 3.15 (0.31), residues: 222 sheet: 0.75 (0.64), residues: 54 loop : 0.57 (0.53), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 104 TYR 0.012 0.001 TYR A 157 PHE 0.010 0.001 PHE A 128 TRP 0.008 0.001 TRP B 56 HIS 0.003 0.001 HIS B 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 3363) covalent geometry : angle 0.52447 / 0.27 ( 4559) SS BOND : bond 0.00018 / 0.01 ( 1) SS BOND : angle 1.03929 / 0.61 ( 2) hydrogen bonds : bond 0.03848 / 2.58 ( 230) hydrogen bonds : angle 5.29063 / 4.01 ( 648) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.121 Fit side-chains REVERT: A 70 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.7224 (ttm-80) REVERT: A 150 LYS cc_start: 0.8343 (tptp) cc_final: 0.8073 (tttm) REVERT: A 157 TYR cc_start: 0.7927 (m-80) cc_final: 0.7025 (t80) REVERT: A 169 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.7993 (mt) REVERT: B 71 SER cc_start: 0.8648 (t) cc_final: 0.8158 (p) REVERT: B 95 TYR cc_start: 0.8518 (m-80) cc_final: 0.8073 (m-80) outliers start: 9 outliers final: 4 residues processed: 64 average time/residue: 0.4090 time to fit residues: 27.2198 Evaluate side-chains 65 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 119 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 3.9990 chunk 15 optimal weight: 0.0570 chunk 1 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 30 optimal weight: 10.0000 chunk 35 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 overall best weight: 0.8502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.178822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.128937 restraints weight = 3337.458| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.75 r_work: 0.3308 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 3364 Z= 0.160 Angle : 0.569 11.011 4561 Z= 0.285 Chirality : 0.043 0.376 506 Planarity : 0.004 0.031 569 Dihedral : 8.102 52.456 497 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.37 % Allowed : 17.75 % Favored : 79.88 % 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: 2.90 (0.39), residues: 410 helix: 3.05 (0.31), residues: 222 sheet: 0.75 (0.63), residues: 54 loop : 0.52 (0.52), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 104 TYR 0.013 0.001 TYR A 157 PHE 0.012 0.002 PHE A 223 TRP 0.008 0.001 TRP B 56 HIS 0.004 0.001 HIS B 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 ( 3363) covalent geometry : angle 0.56856 / 0.29 ( 4559) SS BOND : bond 0.00012 / 0.01 ( 1) SS BOND : angle 1.09522 / 0.64 ( 2) hydrogen bonds : bond 0.04014 / 2.69 ( 230) hydrogen bonds : angle 5.42110 / 4.09 ( 648) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.129 Fit side-chains REVERT: A 70 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.7275 (ttm-80) REVERT: A 150 LYS cc_start: 0.8340 (tptp) cc_final: 0.8080 (tttm) REVERT: A 157 TYR cc_start: 0.7952 (m-80) cc_final: 0.7042 (t80) REVERT: A 169 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8035 (mt) REVERT: B 71 SER cc_start: 0.8667 (t) cc_final: 0.8154 (p) REVERT: B 95 TYR cc_start: 0.8548 (m-80) cc_final: 0.8160 (m-80) outliers start: 8 outliers final: 6 residues processed: 62 average time/residue: 0.4160 time to fit residues: 26.7846 Evaluate side-chains 67 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 119 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 12 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 19 optimal weight: 0.0870 chunk 4 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 31 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 23 optimal weight: 0.3980 chunk 35 optimal weight: 0.0870 overall best weight: 0.3536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.181252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.131987 restraints weight = 3323.403| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.74 r_work: 0.3330 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 3364 Z= 0.114 Angle : 0.533 11.744 4561 Z= 0.261 Chirality : 0.041 0.361 506 Planarity : 0.004 0.031 569 Dihedral : 7.888 53.942 497 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.48 % Allowed : 19.23 % Favored : 79.29 % 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: 3.15 (0.39), residues: 410 helix: 3.29 (0.31), residues: 222 sheet: 0.85 (0.64), residues: 54 loop : 0.55 (0.53), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 104 TYR 0.010 0.001 TYR A 157 PHE 0.009 0.001 PHE A 201 TRP 0.009 0.001 TRP B 111 HIS 0.003 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 ( 3363) covalent geometry : angle 0.53277 / 0.26 ( 4559) SS BOND : bond 0.00061 / 0.03 ( 1) SS BOND : angle 0.89533 / 0.53 ( 2) hydrogen bonds : bond 0.03637 / 2.42 ( 230) hydrogen bonds : angle 5.16864 / 3.91 ( 648) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.123 Fit side-chains REVERT: A 70 ARG cc_start: 0.7718 (OUTLIER) cc_final: 0.7200 (ttm-80) REVERT: A 150 LYS cc_start: 0.8345 (tptp) cc_final: 0.8107 (tttm) REVERT: A 157 TYR cc_start: 0.7871 (m-80) cc_final: 0.7063 (t80) REVERT: A 169 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7977 (mt) REVERT: A 187 ASN cc_start: 0.8497 (t0) cc_final: 0.7765 (m-40) REVERT: B 71 SER cc_start: 0.8628 (t) cc_final: 0.8212 (p) REVERT: B 95 TYR cc_start: 0.8520 (m-80) cc_final: 0.8067 (m-80) outliers start: 5 outliers final: 1 residues processed: 63 average time/residue: 0.3812 time to fit residues: 24.9133 Evaluate side-chains 59 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain B residue 119 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 214 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.178733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.131689 restraints weight = 3350.066| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.23 r_work: 0.3291 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 3364 Z= 0.167 Angle : 0.591 11.589 4561 Z= 0.293 Chirality : 0.044 0.363 506 Planarity : 0.004 0.031 569 Dihedral : 8.072 52.407 497 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.66 % Allowed : 18.05 % Favored : 79.29 % 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 (0.39), residues: 410 helix: 3.12 (0.31), residues: 222 sheet: 0.77 (0.64), residues: 54 loop : 0.45 (0.53), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 104 TYR 0.013 0.001 TYR A 157 PHE 0.015 0.002 PHE A 285 TRP 0.008 0.002 TRP B 56 HIS 0.004 0.001 HIS B 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 ( 3363) covalent geometry : angle 0.59035 / 0.29 ( 4559) SS BOND : bond 0.00014 / 0.01 ( 1) SS BOND : angle 1.11830 / 0.65 ( 2) hydrogen bonds : bond 0.04041 / 2.73 ( 230) hydrogen bonds : angle 5.39399 / 4.07 ( 648) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1580.34 seconds wall clock time: 27 minutes 38.08 seconds (1658.08 seconds total)