Starting phenix.real_space_refine on Wed Jul 1 22:57:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7p16_13157/07_2026/7p16_13157.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p16_13157/07_2026/7p16_13157.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7p16_13157/07_2026/7p16_13157.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7p16_13157/07_2026/7p16_13157.cif" model { file = "/net/cci-nas-00/data/ceres_data/7p16_13157/07_2026/7p16_13157.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p16_13157/07_2026/7p16_13157.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7p16_13157/07_2026/7p16_13157.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p16_13157/07_2026/7p16_13157.map" } resolution = 4.3 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= 0.003 sd= 0.099 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 1 5.49 5 S 23 5.16 5 C 2412 2.51 5 N 561 2.21 5 O 624 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s 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: 3621 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2617 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 7, 'TRANS': 310} Chain breaks: 2 Chain: "B" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 964 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'PLC': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Time building chain proxies: 0.97, per 1000 atoms: 0.27 Number of scatterers: 3621 At special positions: 0 Unit cell: (76.818, 102.858, 70.308, 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 23 16.00 P 1 15.00 O 624 8.00 N 561 7.00 C 2412 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 28 " - pdb=" SG CYS B 102 " 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: 0.29 Conformation dependent library (CDL) restraints added in 138.7 milliseconds 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 824 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 3 sheets defined 68.0% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing helix chain 'A' and resid 4 through 13 removed outlier: 3.587A pdb=" N PHE A 8 " --> pdb=" O THR A 4 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N MET A 10 " --> pdb=" O CYS A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 36 removed outlier: 4.482A pdb=" N THR A 20 " --> pdb=" O ILE A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 67 removed outlier: 3.565A pdb=" N PHE A 47 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL A 48 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL A 55 " --> pdb=" O GLY A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 86 Processing helix chain 'A' and resid 87 through 105 removed outlier: 3.605A pdb=" N PHE A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL A 95 " --> pdb=" O ARG A 91 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A 96 " --> pdb=" O TYR A 92 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N HIS A 101 " --> pdb=" O ARG A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 141 removed outlier: 3.521A pdb=" N LEU A 134 " --> pdb=" O ASP A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 156 removed outlier: 4.092A pdb=" N LEU A 149 " --> pdb=" O PRO A 145 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU A 156 " --> pdb=" O TYR A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 190 removed outlier: 3.723A pdb=" N LEU A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 197 Processing helix chain 'A' and resid 198 through 227 removed outlier: 4.140A pdb=" N LYS A 202 " --> pdb=" O GLY A 198 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU A 214 " --> pdb=" O LEU A 210 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 250 removed outlier: 3.576A pdb=" N VAL A 231 " --> pdb=" O ASP A 227 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE A 247 " --> pdb=" O PHE A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 274 removed outlier: 3.761A pdb=" N VAL A 272 " --> pdb=" O GLY A 268 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N PHE A 273 " --> pdb=" O PHE A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 281 removed outlier: 4.394A pdb=" N GLN A 281 " --> pdb=" O ILE A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 308 removed outlier: 3.513A pdb=" N VAL A 293 " --> pdb=" O CYS A 289 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 343 removed outlier: 3.992A pdb=" N ILE A 319 " --> pdb=" O SER A 315 " (cutoff:3.500A) Proline residue: A 320 - end of helix removed outlier: 3.754A pdb=" N VAL A 326 " --> pdb=" O SER A 322 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU A 329 " --> pdb=" O ILE A 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 71 removed outlier: 3.518A pdb=" N LYS B 71 " --> pdb=" O ASP B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 97 removed outlier: 3.684A pdb=" N THR B 97 " --> pdb=" O PRO B 94 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 9 through 13 Processing sheet with id=AA2, first strand: chain 'B' and resid 17 through 18 removed outlier: 3.588A pdb=" N VAL B 18 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL B 128 " --> pdb=" O ALA B 98 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA B 98 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR B 101 " --> pdb=" O PHE B 43 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA B 55 " --> pdb=" O TRP B 42 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ARG B 44 " --> pdb=" O GLY B 53 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N GLY B 53 " --> pdb=" O ARG B 44 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 17 through 18 removed outlier: 3.588A pdb=" N VAL B 18 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL B 128 " --> pdb=" O ALA B 98 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA B 98 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR B 101 " --> pdb=" O PHE B 43 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA B 105 " --> pdb=" O TYR B 38 " (cutoff:3.500A) 236 hydrogen bonds defined for protein. 678 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: 0.34 Time building geometry restraints manager: 0.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 526 1.31 - 1.44: 1140 1.44 - 1.56: 2016 1.56 - 1.69: 2 1.69 - 1.81: 34 Bond restraints: 3718 Sorted by residual: bond pdb=" C' PLC A 401 " pdb=" O2 PLC A 401 " ideal model delta sigma weight residual 1.332 1.425 -0.093 2.00e-02 2.50e+03 2.17e+01 bond pdb=" CB PLC A 401 " pdb=" O3 PLC A 401 " ideal model delta sigma weight residual 1.327 1.420 -0.093 2.00e-02 2.50e+03 2.15e+01 bond pdb=" C' PLC A 401 " pdb=" C1' PLC A 401 " ideal model delta sigma weight residual 1.503 1.553 -0.050 2.00e-02 2.50e+03 6.23e+00 bond pdb=" C4 PLC A 401 " pdb=" C5 PLC A 401 " ideal model delta sigma weight residual 1.511 1.558 -0.047 2.00e-02 2.50e+03 5.62e+00 bond pdb=" CB PLC A 401 " pdb=" C1B PLC A 401 " ideal model delta sigma weight residual 1.504 1.551 -0.047 2.00e-02 2.50e+03 5.48e+00 ... (remaining 3713 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.21: 5010 3.21 - 6.42: 34 6.42 - 9.64: 5 9.64 - 12.85: 2 12.85 - 16.06: 1 Bond angle restraints: 5052 Sorted by residual: angle pdb=" O3P PLC A 401 " pdb=" P PLC A 401 " pdb=" O4P PLC A 401 " ideal model delta sigma weight residual 93.62 109.68 -16.06 3.00e+00 1.11e-01 2.87e+01 angle pdb=" C5 PLC A 401 " pdb=" N PLC A 401 " pdb=" C7 PLC A 401 " ideal model delta sigma weight residual 106.97 119.04 -12.07 3.00e+00 1.11e-01 1.62e+01 angle pdb=" N LEU B 114 " pdb=" CA LEU B 114 " pdb=" C LEU B 114 " ideal model delta sigma weight residual 114.56 109.89 4.67 1.27e+00 6.20e-01 1.35e+01 angle pdb=" C ILE A 278 " pdb=" N LYS A 279 " pdb=" CA LYS A 279 " ideal model delta sigma weight residual 121.54 128.39 -6.85 1.91e+00 2.74e-01 1.29e+01 angle pdb=" O1P PLC A 401 " pdb=" P PLC A 401 " pdb=" O2P PLC A 401 " ideal model delta sigma weight residual 119.61 109.03 10.58 3.00e+00 1.11e-01 1.24e+01 ... (remaining 5047 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 1891 17.99 - 35.97: 162 35.97 - 53.96: 48 53.96 - 71.95: 5 71.95 - 89.93: 4 Dihedral angle restraints: 2110 sinusoidal: 813 harmonic: 1297 Sorted by residual: dihedral pdb=" CA ILE A 16 " pdb=" C ILE A 16 " pdb=" N ILE A 17 " pdb=" CA ILE A 17 " ideal model delta harmonic sigma weight residual 180.00 160.23 19.77 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CG ARG B 118 " pdb=" CD ARG B 118 " pdb=" NE ARG B 118 " pdb=" CZ ARG B 118 " ideal model delta sinusoidal sigma weight residual 90.00 130.89 -40.89 2 1.50e+01 4.44e-03 9.14e+00 dihedral pdb=" CB GLU A 260 " pdb=" CG GLU A 260 " pdb=" CD GLU A 260 " pdb=" OE1 GLU A 260 " ideal model delta sinusoidal sigma weight residual 0.00 -81.53 81.53 1 3.00e+01 1.11e-03 9.09e+00 ... (remaining 2107 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 385 0.033 - 0.067: 148 0.067 - 0.100: 30 0.100 - 0.133: 8 0.133 - 0.166: 1 Chirality restraints: 572 Sorted by residual: chirality pdb=" C2 PLC A 401 " pdb=" C1 PLC A 401 " pdb=" C3 PLC A 401 " pdb=" O2 PLC A 401 " both_signs ideal model delta sigma weight residual False -2.31 -2.48 0.17 2.00e-01 2.50e+01 6.91e-01 chirality pdb=" CG LEU B 87 " pdb=" CB LEU B 87 " pdb=" CD1 LEU B 87 " pdb=" CD2 LEU B 87 " both_signs ideal model delta sigma weight residual False -2.59 -2.71 0.12 2.00e-01 2.50e+01 3.62e-01 chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.28e-01 ... (remaining 569 not shown) Planarity restraints: 604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 190 " 0.027 5.00e-02 4.00e+02 4.06e-02 2.64e+00 pdb=" N PRO A 191 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 191 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 191 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 73 " 0.130 9.50e-02 1.11e+02 5.86e-02 2.24e+00 pdb=" NE ARG B 73 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG B 73 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG B 73 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 73 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 123 " 0.006 2.00e-02 2.50e+03 1.29e-02 1.65e+00 pdb=" CD GLU A 123 " -0.022 2.00e-02 2.50e+03 pdb=" OE1 GLU A 123 " 0.008 2.00e-02 2.50e+03 pdb=" OE2 GLU A 123 " 0.008 2.00e-02 2.50e+03 ... (remaining 601 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 100 2.72 - 3.27: 3862 3.27 - 3.81: 5788 3.81 - 4.36: 6594 4.36 - 4.90: 11142 Nonbonded interactions: 27486 Sorted by model distance: nonbonded pdb=" O THR A 139 " pdb=" N GLY A 143 " model vdw 2.178 3.120 nonbonded pdb=" NZ LYS A 209 " pdb=" OG1 THR A 274 " model vdw 2.261 3.120 nonbonded pdb=" OG SER A 132 " pdb=" OD2 ASP A 181 " model vdw 2.291 3.040 nonbonded pdb=" OE1 GLU B 12 " pdb=" N GLY B 125 " model vdw 2.347 3.120 nonbonded pdb=" O CYS B 28 " pdb=" OG1 THR B 84 " model vdw 2.357 3.040 ... (remaining 27481 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.020 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 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 : 0.004 0.093 3719 Z= 0.205 Angle : 0.733 16.060 5054 Z= 0.340 Chirality : 0.037 0.166 572 Planarity : 0.004 0.059 604 Dihedral : 15.072 89.932 1283 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % 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: -0.08 (0.40), residues: 436 helix: 0.55 (0.32), residues: 249 sheet: 0.04 (0.84), residues: 44 loop : -1.00 (0.54), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 264 TYR 0.017 0.001 TYR A 92 PHE 0.016 0.001 PHE A 275 TRP 0.007 0.001 TRP A 177 HIS 0.001 0.000 HIS A 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.21 ( 3718) covalent geometry : angle 0.73320 / 0.34 ( 5052) SS BOND : bond 0.00141 / 0.07 ( 1) SS BOND : angle 0.38125 / 0.21 ( 2) hydrogen bonds : bond 0.27497 / 18.04 ( 231) hydrogen bonds : angle 8.01179 / 5.83 ( 678) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.126 Fit side-chains REVERT: A 146 GLN cc_start: 0.9242 (tm-30) cc_final: 0.8783 (tm-30) REVERT: A 279 LYS cc_start: 0.7233 (tttt) cc_final: 0.6998 (mttt) REVERT: B 42 TRP cc_start: 0.8513 (m100) cc_final: 0.7949 (m100) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.0720 time to fit residues: 11.5239 Evaluate side-chains 114 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 0.0060 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 183 GLN A 277 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.166116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.136534 restraints weight = 5154.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.135494 restraints weight = 7766.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.135710 restraints weight = 7542.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.136165 restraints weight = 6322.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.136296 restraints weight = 5452.002| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3719 Z= 0.140 Angle : 0.586 6.716 5054 Z= 0.301 Chirality : 0.040 0.139 572 Planarity : 0.004 0.053 604 Dihedral : 6.472 59.884 510 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.26 % Allowed : 5.41 % Favored : 94.33 % 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: 0.69 (0.40), residues: 436 helix: 1.16 (0.30), residues: 260 sheet: 0.56 (0.79), residues: 50 loop : -0.98 (0.61), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 264 TYR 0.018 0.001 TYR A 208 PHE 0.023 0.001 PHE A 225 TRP 0.007 0.001 TRP A 177 HIS 0.001 0.000 HIS A 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 ( 3718) covalent geometry : angle 0.58597 / 0.30 ( 5052) SS BOND : bond 0.00139 / 0.07 ( 1) SS BOND : angle 0.24610 / 0.14 ( 2) hydrogen bonds : bond 0.04649 / 3.13 ( 231) hydrogen bonds : angle 4.58351 / 3.29 ( 678) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 140 time to evaluate : 0.166 Fit side-chains REVERT: A 259 MET cc_start: 0.8119 (mmp) cc_final: 0.7710 (mmp) REVERT: B 37 ILE cc_start: 0.9156 (mm) cc_final: 0.8661 (mt) outliers start: 1 outliers final: 0 residues processed: 141 average time/residue: 0.0681 time to fit residues: 11.9035 Evaluate side-chains 116 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 26 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 9 optimal weight: 6.9990 chunk 33 optimal weight: 0.3980 chunk 40 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 7 optimal weight: 7.9990 chunk 32 optimal weight: 8.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 HIS ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.163630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.134469 restraints weight = 5200.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.132322 restraints weight = 7713.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.132960 restraints weight = 7570.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.133117 restraints weight = 6704.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.133176 restraints weight = 6615.180| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3719 Z= 0.169 Angle : 0.601 7.398 5054 Z= 0.305 Chirality : 0.041 0.145 572 Planarity : 0.004 0.050 604 Dihedral : 6.063 56.379 510 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % 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: 0.67 (0.40), residues: 436 helix: 1.22 (0.30), residues: 262 sheet: 0.60 (0.92), residues: 37 loop : -1.06 (0.56), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 264 TYR 0.019 0.002 TYR A 92 PHE 0.017 0.001 PHE A 47 TRP 0.008 0.001 TRP A 177 HIS 0.002 0.001 HIS A 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 ( 3718) covalent geometry : angle 0.60084 / 0.30 ( 5052) SS BOND : bond 0.00065 / 0.03 ( 1) SS BOND : angle 0.24831 / 0.13 ( 2) hydrogen bonds : bond 0.04191 / 2.80 ( 231) hydrogen bonds : angle 4.36939 / 3.10 ( 678) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.140 Fit side-chains REVERT: A 166 MET cc_start: 0.7405 (tmm) cc_final: 0.7180 (tmm) REVERT: A 202 LYS cc_start: 0.8495 (mttt) cc_final: 0.8269 (mttt) REVERT: B 52 GLU cc_start: 0.7705 (pm20) cc_final: 0.7473 (pm20) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.0680 time to fit residues: 11.2957 Evaluate side-chains 117 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 39 optimal weight: 0.6980 chunk 6 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.168072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.141437 restraints weight = 5115.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.139337 restraints weight = 8284.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.139923 restraints weight = 7967.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.139516 restraints weight = 6617.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.139831 restraints weight = 5849.592| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3719 Z= 0.141 Angle : 0.588 7.387 5054 Z= 0.296 Chirality : 0.040 0.144 572 Planarity : 0.004 0.054 604 Dihedral : 5.636 55.297 510 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % 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: 0.67 (0.40), residues: 436 helix: 1.28 (0.30), residues: 264 sheet: 0.22 (0.75), residues: 50 loop : -1.24 (0.60), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 157 TYR 0.018 0.001 TYR A 92 PHE 0.014 0.001 PHE A 47 TRP 0.010 0.001 TRP A 177 HIS 0.003 0.001 HIS A 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 3718) covalent geometry : angle 0.58786 / 0.30 ( 5052) SS BOND : bond 0.00339 / 0.18 ( 1) SS BOND : angle 0.21788 / 0.12 ( 2) hydrogen bonds : bond 0.03673 / 2.42 ( 231) hydrogen bonds : angle 4.05462 / 2.85 ( 678) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.077 Fit side-chains REVERT: A 91 ARG cc_start: 0.7192 (ttm110) cc_final: 0.6884 (ttm110) REVERT: A 140 TYR cc_start: 0.9337 (m-80) cc_final: 0.9084 (m-10) REVERT: B 52 GLU cc_start: 0.7781 (pm20) cc_final: 0.7564 (pm20) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.0617 time to fit residues: 10.7477 Evaluate side-chains 117 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 34 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 9 optimal weight: 8.9990 chunk 27 optimal weight: 0.9980 chunk 38 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.161694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.132849 restraints weight = 5298.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.130446 restraints weight = 4891.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.129728 restraints weight = 6001.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.129658 restraints weight = 5939.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.129638 restraints weight = 5923.729| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3719 Z= 0.204 Angle : 0.674 7.480 5054 Z= 0.335 Chirality : 0.043 0.191 572 Planarity : 0.004 0.054 604 Dihedral : 6.011 58.392 510 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % 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: 0.67 (0.40), residues: 436 helix: 1.24 (0.30), residues: 264 sheet: 0.46 (0.79), residues: 45 loop : -1.20 (0.59), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 197 TYR 0.021 0.002 TYR A 92 PHE 0.015 0.002 PHE B 43 TRP 0.014 0.001 TRP A 177 HIS 0.003 0.001 HIS A 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.20 ( 3718) covalent geometry : angle 0.67436 / 0.33 ( 5052) SS BOND : bond 0.00028 / 0.01 ( 1) SS BOND : angle 0.62580 / 0.33 ( 2) hydrogen bonds : bond 0.03891 / 2.56 ( 231) hydrogen bonds : angle 4.21023 / 2.94 ( 678) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.080 Fit side-chains REVERT: A 166 MET cc_start: 0.7336 (tmm) cc_final: 0.7104 (tmm) REVERT: B 42 TRP cc_start: 0.8630 (m100) cc_final: 0.7927 (m100) REVERT: B 51 ARG cc_start: 0.7775 (mtt180) cc_final: 0.7546 (mtt180) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.0401 time to fit residues: 6.6686 Evaluate side-chains 117 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 42 optimal weight: 0.1980 chunk 36 optimal weight: 0.2980 chunk 18 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 38 optimal weight: 7.9990 chunk 5 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.165275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.138545 restraints weight = 5271.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.136471 restraints weight = 9627.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.137247 restraints weight = 9871.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.137323 restraints weight = 7080.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.137418 restraints weight = 6655.686| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3719 Z= 0.130 Angle : 0.608 7.473 5054 Z= 0.300 Chirality : 0.039 0.136 572 Planarity : 0.004 0.056 604 Dihedral : 5.779 59.160 510 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % 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: 0.77 (0.41), residues: 436 helix: 1.31 (0.30), residues: 264 sheet: 0.31 (0.70), residues: 59 loop : -1.18 (0.66), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 157 TYR 0.024 0.002 TYR B 39 PHE 0.011 0.001 PHE A 225 TRP 0.019 0.001 TRP A 62 HIS 0.002 0.001 HIS A 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 3718) covalent geometry : angle 0.60848 / 0.30 ( 5052) SS BOND : bond 0.00163 / 0.09 ( 1) SS BOND : angle 0.42318 / 0.22 ( 2) hydrogen bonds : bond 0.03455 / 2.26 ( 231) hydrogen bonds : angle 3.95749 / 2.78 ( 678) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.140 Fit side-chains REVERT: B 97 THR cc_start: 0.8612 (m) cc_final: 0.8405 (m) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.0668 time to fit residues: 10.9973 Evaluate side-chains 115 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 15 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 40 optimal weight: 7.9990 chunk 8 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 27 optimal weight: 0.2980 chunk 33 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.164116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.139462 restraints weight = 5426.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.137351 restraints weight = 10105.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.134844 restraints weight = 9598.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.133011 restraints weight = 7063.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.133295 restraints weight = 7265.052| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3719 Z= 0.155 Angle : 0.635 7.428 5054 Z= 0.312 Chirality : 0.041 0.152 572 Planarity : 0.004 0.057 604 Dihedral : 5.835 59.880 510 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % 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: 0.64 (0.41), residues: 436 helix: 1.27 (0.30), residues: 266 sheet: 0.12 (0.74), residues: 50 loop : -1.28 (0.62), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 264 TYR 0.021 0.002 TYR A 92 PHE 0.022 0.001 PHE A 47 TRP 0.012 0.001 TRP A 177 HIS 0.002 0.001 HIS A 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 ( 3718) covalent geometry : angle 0.63534 / 0.31 ( 5052) SS BOND : bond 0.00038 / 0.02 ( 1) SS BOND : angle 0.36581 / 0.19 ( 2) hydrogen bonds : bond 0.03614 / 2.35 ( 231) hydrogen bonds : angle 4.01967 / 2.82 ( 678) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.079 Fit side-chains REVERT: A 95 VAL cc_start: 0.7957 (m) cc_final: 0.5748 (m) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.0616 time to fit residues: 9.9410 Evaluate side-chains 113 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 5 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 HIS A 121 HIS A 183 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.169606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.141850 restraints weight = 5344.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.139037 restraints weight = 8089.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.139645 restraints weight = 8218.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.139832 restraints weight = 6698.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.139990 restraints weight = 6211.102| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3719 Z= 0.152 Angle : 0.648 7.523 5054 Z= 0.322 Chirality : 0.041 0.144 572 Planarity : 0.004 0.060 604 Dihedral : 5.864 59.777 510 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.41), residues: 436 helix: 1.15 (0.31), residues: 266 sheet: 0.26 (0.72), residues: 59 loop : -1.24 (0.67), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 264 TYR 0.034 0.002 TYR A 92 PHE 0.026 0.001 PHE A 47 TRP 0.013 0.001 TRP A 177 HIS 0.003 0.001 HIS A 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 ( 3718) covalent geometry : angle 0.64796 / 0.32 ( 5052) SS BOND : bond 0.00341 / 0.18 ( 1) SS BOND : angle 0.47820 / 0.25 ( 2) hydrogen bonds : bond 0.03483 / 2.29 ( 231) hydrogen bonds : angle 4.07739 / 2.88 ( 678) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.141 Fit side-chains REVERT: A 187 ARG cc_start: 0.6595 (ttt180) cc_final: 0.6261 (ttp-170) REVERT: A 260 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7076 (mm-30) REVERT: A 264 ARG cc_start: 0.7859 (mmm-85) cc_final: 0.7391 (mtt90) REVERT: A 343 TYR cc_start: 0.7440 (m-80) cc_final: 0.7176 (m-80) REVERT: B 42 TRP cc_start: 0.8519 (m100) cc_final: 0.7899 (m100) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.0655 time to fit residues: 10.9075 Evaluate side-chains 115 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 9 optimal weight: 0.0870 chunk 13 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 16 optimal weight: 10.0000 chunk 17 optimal weight: 0.1980 chunk 14 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 HIS A 121 HIS A 150 GLN B 88 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.166564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.140003 restraints weight = 5225.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.138653 restraints weight = 8760.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.138924 restraints weight = 8048.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.139041 restraints weight = 6552.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.139157 restraints weight = 5849.134| |-----------------------------------------------------------------------------| r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3719 Z= 0.135 Angle : 0.650 8.012 5054 Z= 0.317 Chirality : 0.041 0.177 572 Planarity : 0.004 0.060 604 Dihedral : 5.711 57.875 510 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.26 % Allowed : 0.77 % Favored : 98.97 % 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: 0.53 (0.41), residues: 436 helix: 1.15 (0.30), residues: 267 sheet: 0.14 (0.70), residues: 59 loop : -1.41 (0.66), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 264 TYR 0.033 0.002 TYR A 92 PHE 0.023 0.001 PHE A 47 TRP 0.014 0.001 TRP A 177 HIS 0.002 0.001 HIS A 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 3718) covalent geometry : angle 0.65034 / 0.32 ( 5052) SS BOND : bond 0.00231 / 0.12 ( 1) SS BOND : angle 0.24358 / 0.14 ( 2) hydrogen bonds : bond 0.03398 / 2.23 ( 231) hydrogen bonds : angle 3.98031 / 2.83 ( 678) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 0.156 Fit side-chains REVERT: A 187 ARG cc_start: 0.6382 (ttt180) cc_final: 0.6067 (ttp-170) REVERT: A 248 ILE cc_start: 0.8544 (tp) cc_final: 0.8321 (tp) REVERT: A 260 GLU cc_start: 0.7768 (mm-30) cc_final: 0.6992 (mm-30) REVERT: A 264 ARG cc_start: 0.7801 (mmm-85) cc_final: 0.7403 (mtt90) REVERT: A 343 TYR cc_start: 0.7224 (m-80) cc_final: 0.6951 (m-80) REVERT: B 42 TRP cc_start: 0.8430 (m100) cc_final: 0.7805 (m100) REVERT: B 93 LYS cc_start: 0.6387 (pttt) cc_final: 0.5506 (pttt) outliers start: 1 outliers final: 0 residues processed: 131 average time/residue: 0.0561 time to fit residues: 9.2631 Evaluate side-chains 109 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 42 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 HIS A 121 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.169706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.141535 restraints weight = 5399.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.140458 restraints weight = 8903.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.142341 restraints weight = 8318.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.142019 restraints weight = 5497.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.142465 restraints weight = 5123.703| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3719 Z= 0.162 Angle : 0.688 8.598 5054 Z= 0.339 Chirality : 0.042 0.149 572 Planarity : 0.004 0.059 604 Dihedral : 5.795 58.692 510 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % 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: 0.53 (0.41), residues: 436 helix: 1.18 (0.30), residues: 266 sheet: 0.01 (0.75), residues: 50 loop : -1.30 (0.63), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 264 TYR 0.034 0.002 TYR A 92 PHE 0.024 0.001 PHE A 47 TRP 0.036 0.002 TRP A 93 HIS 0.002 0.001 HIS A 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 ( 3718) covalent geometry : angle 0.68790 / 0.34 ( 5052) SS BOND : bond 0.00020 / 0.01 ( 1) SS BOND : angle 0.46532 / 0.25 ( 2) hydrogen bonds : bond 0.03618 / 2.32 ( 231) hydrogen bonds : angle 4.03872 / 2.85 ( 678) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.126 Fit side-chains REVERT: A 248 ILE cc_start: 0.8526 (tp) cc_final: 0.8319 (tp) REVERT: A 260 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7043 (mm-30) REVERT: A 264 ARG cc_start: 0.7839 (mmm-85) cc_final: 0.7410 (mtt90) REVERT: A 343 TYR cc_start: 0.7208 (m-80) cc_final: 0.6979 (m-80) REVERT: B 37 ILE cc_start: 0.9173 (mm) cc_final: 0.8922 (mm) REVERT: B 93 LYS cc_start: 0.6529 (pttt) cc_final: 0.5647 (pttt) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.0543 time to fit residues: 9.0607 Evaluate side-chains 113 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 18 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.162714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.133013 restraints weight = 5245.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.129826 restraints weight = 10446.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.130311 restraints weight = 10057.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.129300 restraints weight = 8942.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.130020 restraints weight = 7612.044| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3719 Z= 0.177 Angle : 0.702 8.603 5054 Z= 0.345 Chirality : 0.043 0.171 572 Planarity : 0.005 0.059 604 Dihedral : 5.901 59.701 510 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % 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: 0.52 (0.41), residues: 436 helix: 1.14 (0.30), residues: 266 sheet: 0.12 (0.72), residues: 59 loop : -1.36 (0.67), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 91 TYR 0.030 0.002 TYR A 92 PHE 0.025 0.002 PHE A 47 TRP 0.023 0.002 TRP A 177 HIS 0.002 0.000 HIS A 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 ( 3718) covalent geometry : angle 0.70201 / 0.34 ( 5052) SS BOND : bond 0.00023 / 0.01 ( 1) SS BOND : angle 0.59342 / 0.31 ( 2) hydrogen bonds : bond 0.03617 / 2.36 ( 231) hydrogen bonds : angle 4.14187 / 2.91 ( 678) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 773.76 seconds wall clock time: 14 minutes 3.91 seconds (843.91 seconds total)