Starting phenix.real_space_refine on Tue Aug 4 12:22:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iyx_61003/08_2026/9iyx_61003.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iyx_61003/08_2026/9iyx_61003.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9iyx_61003/08_2026/9iyx_61003.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iyx_61003/08_2026/9iyx_61003.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9iyx_61003/08_2026/9iyx_61003.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iyx_61003/08_2026/9iyx_61003.map" } resolution = 3.6 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= 0.043 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 Zn 2 6.06 5 S 18 5.16 5 C 1772 2.51 5 N 414 2.21 5 O 420 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 2626 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1302 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 16, 'TRANS': 162} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 234 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'ASN:plan1': 2, 'PHE:plan': 5, 'TRP:plan': 4, 'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 83 Chain: "B" Number of atoms: 1322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1322 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 16, 'TRANS': 155} Chain breaks: 2 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 2, 'TRP:plan': 3, 'PHE:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 347 SG CYS A 48 56.811 25.413 16.460 1.00 2.92 S ATOM 417 SG CYS A 65 53.101 25.858 17.554 1.00 3.68 S ATOM 442 SG CYS A 69 54.091 23.123 15.110 1.00 3.57 S ATOM 1605 SG CYS B 48 68.977 38.696 20.531 1.00 1.71 S ATOM 1673 SG CYS B 65 70.381 38.605 24.224 1.00 1.25 S ATOM 1700 SG CYS B 69 72.048 40.812 21.357 1.00 1.49 S Time building chain proxies: 0.92, per 1000 atoms: 0.35 Number of scatterers: 2626 At special positions: 0 Unit cell: (98.072, 75.686, 79.95, 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) Zn 2 29.99 S 18 16.00 O 420 8.00 N 414 7.00 C 1772 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.17 Conformation dependent library (CDL) restraints added in 64.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" NE2 HIS A 60 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 69 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 65 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 48 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 60 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 48 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 69 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 65 " Number of angles added : 6 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 660 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 0 sheets defined 79.5% alpha, 0.0% 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 3 through 26 Proline residue: A 11 - end of helix Processing helix chain 'A' and resid 27 through 41 removed outlier: 3.567A pdb=" N PHE A 41 " --> pdb=" O THR A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 99 removed outlier: 4.214A pdb=" N TRP A 74 " --> pdb=" O PRO A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 102 No H-bonds generated for 'chain 'A' and resid 100 through 102' Processing helix chain 'A' and resid 156 through 170 Processing helix chain 'A' and resid 170 through 186 removed outlier: 4.402A pdb=" N SER A 174 " --> pdb=" O PHE A 170 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU A 175 " --> pdb=" O SER A 171 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU A 176 " --> pdb=" O TRP A 172 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 187 through 207 Proline residue: A 203 - end of helix Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 211 through 226 removed outlier: 3.696A pdb=" N LEU A 215 " --> pdb=" O PRO A 211 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU A 216 " --> pdb=" O PHE A 212 " (cutoff:3.500A) Proline residue: A 217 - end of helix Processing helix chain 'B' and resid 10 through 41 Proline residue: B 29 - end of helix removed outlier: 3.752A pdb=" N PHE B 41 " --> pdb=" O THR B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 102 removed outlier: 4.276A pdb=" N ARG B 73 " --> pdb=" O CYS B 69 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N TRP B 74 " --> pdb=" O PRO B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 171 Processing helix chain 'B' and resid 172 through 186 Proline residue: B 178 - end of helix Processing helix chain 'B' and resid 189 through 210 removed outlier: 3.590A pdb=" N SER B 193 " --> pdb=" O THR B 189 " (cutoff:3.500A) Proline residue: B 203 - end of helix Processing helix chain 'B' and resid 211 through 213 No H-bonds generated for 'chain 'B' and resid 211 through 213' Processing helix chain 'B' and resid 214 through 226 removed outlier: 3.723A pdb=" N ILE B 218 " --> pdb=" O PRO B 214 " (cutoff:3.500A) 184 hydrogen bonds defined for protein. 552 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: 0.38 Time building geometry restraints manager: 0.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 386 1.32 - 1.44: 814 1.44 - 1.57: 1496 1.57 - 1.69: 1 1.69 - 1.81: 24 Bond restraints: 2721 Sorted by residual: bond pdb=" CA THR A 46 " pdb=" C THR A 46 " ideal model delta sigma weight residual 1.523 1.581 -0.058 1.34e-02 5.57e+03 1.86e+01 bond pdb=" N THR A 46 " pdb=" CA THR A 46 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.29e-02 6.01e+03 1.00e+01 bond pdb=" CA THR A 45 " pdb=" C THR A 45 " ideal model delta sigma weight residual 1.524 1.560 -0.036 1.26e-02 6.30e+03 8.35e+00 bond pdb=" C ASN A 40 " pdb=" O ASN A 40 " ideal model delta sigma weight residual 1.236 1.201 0.035 1.25e-02 6.40e+03 7.98e+00 bond pdb=" CA PHE A 41 " pdb=" C PHE A 41 " ideal model delta sigma weight residual 1.531 1.499 0.032 1.46e-02 4.69e+03 4.89e+00 ... (remaining 2716 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 3645 2.19 - 4.38: 89 4.38 - 6.57: 12 6.57 - 8.76: 1 8.76 - 10.95: 1 Bond angle restraints: 3748 Sorted by residual: angle pdb=" N THR A 45 " pdb=" CA THR A 45 " pdb=" C THR A 45 " ideal model delta sigma weight residual 111.14 122.09 -10.95 1.08e+00 8.57e-01 1.03e+02 angle pdb=" C ASN A 40 " pdb=" N PHE A 41 " pdb=" CA PHE A 41 " ideal model delta sigma weight residual 123.03 118.01 5.02 1.34e+00 5.57e-01 1.40e+01 angle pdb=" CA THR A 46 " pdb=" C THR A 46 " pdb=" N VAL A 47 " ideal model delta sigma weight residual 116.84 122.76 -5.92 1.71e+00 3.42e-01 1.20e+01 angle pdb=" C PHE A 41 " pdb=" CA PHE A 41 " pdb=" CB PHE A 41 " ideal model delta sigma weight residual 111.85 106.87 4.98 1.47e+00 4.63e-01 1.15e+01 angle pdb=" C MET B 198 " pdb=" N TRP B 199 " pdb=" CA TRP B 199 " ideal model delta sigma weight residual 120.28 124.53 -4.25 1.34e+00 5.57e-01 1.01e+01 ... (remaining 3743 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.12: 1382 15.12 - 30.23: 119 30.23 - 45.35: 30 45.35 - 60.47: 2 60.47 - 75.58: 2 Dihedral angle restraints: 1535 sinusoidal: 522 harmonic: 1013 Sorted by residual: dihedral pdb=" C THR A 46 " pdb=" N THR A 46 " pdb=" CA THR A 46 " pdb=" CB THR A 46 " ideal model delta harmonic sigma weight residual -122.00 -134.41 12.41 0 2.50e+00 1.60e-01 2.46e+01 dihedral pdb=" N THR A 46 " pdb=" C THR A 46 " pdb=" CA THR A 46 " pdb=" CB THR A 46 " ideal model delta harmonic sigma weight residual 123.40 132.57 -9.17 0 2.50e+00 1.60e-01 1.34e+01 dihedral pdb=" CB MET B 75 " pdb=" CG MET B 75 " pdb=" SD MET B 75 " pdb=" CE MET B 75 " ideal model delta sinusoidal sigma weight residual 180.00 129.77 50.23 3 1.50e+01 4.44e-03 8.87e+00 ... (remaining 1532 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 350 0.054 - 0.109: 64 0.109 - 0.163: 14 0.163 - 0.217: 1 0.217 - 0.272: 1 Chirality restraints: 430 Sorted by residual: chirality pdb=" CA THR A 46 " pdb=" N THR A 46 " pdb=" C THR A 46 " pdb=" CB THR A 46 " both_signs ideal model delta sigma weight residual False 2.53 2.25 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CA THR A 45 " pdb=" N THR A 45 " pdb=" C THR A 45 " pdb=" CB THR A 45 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.19 2.00e-01 2.50e+01 9.10e-01 chirality pdb=" CA ASN B 59 " pdb=" N ASN B 59 " pdb=" C ASN B 59 " pdb=" CB ASN B 59 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.23e-01 ... (remaining 427 not shown) Planarity restraints: 454 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 65 " 0.041 5.00e-02 4.00e+02 6.36e-02 6.46e+00 pdb=" N PRO A 66 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 66 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 66 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 44 " -0.012 2.00e-02 2.50e+03 2.38e-02 5.65e+00 pdb=" C GLY A 44 " 0.041 2.00e-02 2.50e+03 pdb=" O GLY A 44 " -0.016 2.00e-02 2.50e+03 pdb=" N THR A 45 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 216 " 0.036 5.00e-02 4.00e+02 5.52e-02 4.88e+00 pdb=" N PRO B 217 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 217 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 217 " 0.031 5.00e-02 4.00e+02 ... (remaining 451 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 52 2.69 - 3.24: 2972 3.24 - 3.79: 4240 3.79 - 4.35: 5062 4.35 - 4.90: 7896 Nonbonded interactions: 20222 Sorted by model distance: nonbonded pdb=" O TRP A 35 " pdb=" OG SER A 38 " model vdw 2.132 3.040 nonbonded pdb=" OE1 GLN B 30 " pdb=" NH2 ARG B 79 " model vdw 2.138 3.120 nonbonded pdb=" O TRP A 201 " pdb=" N LEU A 205 " model vdw 2.156 3.120 nonbonded pdb=" O PRO A 62 " pdb=" NH2 ARG A 78 " model vdw 2.187 3.120 nonbonded pdb=" O PHE B 170 " pdb=" OG SER B 171 " model vdw 2.238 3.040 ... (remaining 20217 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 9 through 11 or (resid 12 through 13 and (name N or name C \ A or name C or name O or name CB )) or resid 14 through 15 or (resid 16 through \ 17 and (name N or name CA or name C or name O or name CB )) or resid 18 through \ 50 or resid 58 through 178 or (resid 179 through 181 and (name N or name CA or n \ ame C or name O or name CB )) or resid 182 through 1001)) selection = (chain 'B' and (resid 9 through 12 or (resid 13 and (name N or name CA or name C \ or name O or name CB )) or resid 14 through 58 or (resid 59 and (name N or name \ CA or name C or name O or name CB )) or resid 60 through 67 or (resid 68 and (n \ ame N or name CA or name C or name O or name CB )) or resid 69 through 169 or (r \ esid 170 through 177 and (name N or name CA or name C or name O or name CB )) or \ resid 178 through 182 or (resid 183 through 184 and (name N or name CA or name \ C or name O or name CB )) or resid 185 through 188 or (resid 189 through 194 and \ (name N or name CA or name C or name O or name CB )) or resid 195 through 196 o \ r (resid 197 through 198 and (name N or name CA or name C or name O or name CB ) \ ) or resid 199 through 200 or (resid 201 and (name N or name CA or name C or nam \ e O or name CB )) or resid 202 through 203 or (resid 204 through 205 and (name N \ or name CA or name C or name O or name CB )) or resid 206 or (resid 207 through \ 210 and (name N or name CA or name C or name O or name CB )) or resid 211 or (r \ esid 212 through 213 and (name N or name CA or name C or name O or name CB )) or \ resid 214 through 216 or (resid 217 and (name N or name CA or name C or name O \ or name CB )) or resid 218 or (resid 219 through 226 and (name N or name CA or n \ ame C or name O or name CB )) or resid 301)) } 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: 2.860 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: 0.010 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.850 Find NCS groups from input model: 0.050 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6731 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 : 0.005 0.058 2729 Z= 0.250 Angle : 0.791 10.952 3754 Z= 0.473 Chirality : 0.044 0.272 430 Planarity : 0.009 0.064 454 Dihedral : 12.810 75.584 875 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.40 % Allowed : 0.79 % Favored : 98.81 % Cbeta Deviations : 0.30 % 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: 1.26 (0.49), residues: 339 helix: 0.99 (0.34), residues: 244 sheet: None (None), residues: 0 loop : 0.76 (0.74), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 73 TYR 0.008 0.001 TYR B 200 PHE 0.018 0.002 PHE B 219 TRP 0.013 0.001 TRP B 36 HIS 0.004 0.002 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.25 ( 2721) covalent geometry : angle 0.78017 / 0.47 ( 3748) hydrogen bonds : bond 0.17505 / 10.60 ( 184) hydrogen bonds : angle 7.90669 / 5.82 ( 552) metal coordination : bond 0.01410 / 1.05 ( 8) metal coordination : angle 3.35346 / 1.60 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 0.096 Fit side-chains REVERT: A 103 MET cc_start: 0.7181 (tpp) cc_final: 0.6956 (tpp) outliers start: 1 outliers final: 1 residues processed: 61 average time/residue: 0.0417 time to fit residues: 3.1843 Evaluate side-chains 51 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 50 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 24 optimal weight: 0.3980 chunk 26 optimal weight: 0.4980 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.2980 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 0.0870 chunk 22 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 70.8835 > 50:) chunk 13 optimal weight: 8.9990 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 GLN B 59 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.199503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.168307 restraints weight = 4052.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.169425 restraints weight = 3428.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.169626 restraints weight = 2976.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.169626 restraints weight = 2821.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.169626 restraints weight = 2821.106| |-----------------------------------------------------------------------------| r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 2729 Z= 0.166 Angle : 0.690 7.587 3754 Z= 0.334 Chirality : 0.045 0.153 430 Planarity : 0.008 0.053 454 Dihedral : 5.980 78.906 366 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.37 % Allowed : 9.49 % Favored : 88.14 % 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: 3.11 (0.46), residues: 339 helix: 2.20 (0.31), residues: 252 sheet: None (None), residues: 0 loop : 1.89 (0.81), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 73 TYR 0.006 0.001 TYR B 200 PHE 0.024 0.002 PHE B 93 TRP 0.011 0.001 TRP A 163 HIS 0.004 0.002 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 ( 2721) covalent geometry : angle 0.68307 / 0.33 ( 3748) hydrogen bonds : bond 0.04264 / 2.81 ( 184) hydrogen bonds : angle 4.81681 / 3.43 ( 552) metal coordination : bond 0.01117 / 0.76 ( 8) metal coordination : angle 2.48384 / 1.28 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.058 Fit side-chains REVERT: A 103 MET cc_start: 0.7126 (tpp) cc_final: 0.6782 (tpp) outliers start: 6 outliers final: 2 residues processed: 57 average time/residue: 0.0264 time to fit residues: 1.9753 Evaluate side-chains 48 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 46 time to evaluate : 0.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 87 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 16 optimal weight: 0.0000 chunk 21 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 26 optimal weight: 0.3980 chunk 4 optimal weight: 0.9990 chunk 33 optimal weight: 0.0170 chunk 31 optimal weight: 0.9990 chunk 2 optimal weight: 0.3980 chunk 14 optimal weight: 0.6980 overall best weight: 0.3022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.197419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.168235 restraints weight = 4058.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.169038 restraints weight = 3284.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.169286 restraints weight = 2864.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.169381 restraints weight = 2657.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.169390 restraints weight = 2573.328| |-----------------------------------------------------------------------------| r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 2729 Z= 0.135 Angle : 0.651 9.600 3754 Z= 0.306 Chirality : 0.043 0.151 430 Planarity : 0.007 0.052 454 Dihedral : 5.808 78.164 364 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.16 % Allowed : 11.86 % Favored : 84.98 % 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: 3.35 (0.46), residues: 339 helix: 2.43 (0.32), residues: 252 sheet: None (None), residues: 0 loop : 1.82 (0.79), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 79 TYR 0.007 0.001 TYR B 200 PHE 0.025 0.002 PHE B 219 TRP 0.009 0.001 TRP A 163 HIS 0.004 0.002 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.13 ( 2721) covalent geometry : angle 0.64480 / 0.30 ( 3748) hydrogen bonds : bond 0.03443 / 2.24 ( 184) hydrogen bonds : angle 4.25772 / 3.03 ( 552) metal coordination : bond 0.00678 / 0.51 ( 8) metal coordination : angle 2.29961 / 1.24 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.094 Fit side-chains REVERT: A 103 MET cc_start: 0.7040 (tpp) cc_final: 0.6731 (tpp) outliers start: 8 outliers final: 4 residues processed: 53 average time/residue: 0.0394 time to fit residues: 2.7904 Evaluate side-chains 53 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 189 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 17 optimal weight: 2.9990 chunk 26 optimal weight: 0.0010 chunk 3 optimal weight: 0.2980 chunk 15 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 23 optimal weight: 0.3980 chunk 18 optimal weight: 0.4980 chunk 16 optimal weight: 1.9990 overall best weight: 0.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.195300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.165987 restraints weight = 4120.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.166961 restraints weight = 3366.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.166961 restraints weight = 2969.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.166961 restraints weight = 2969.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.166961 restraints weight = 2969.705| |-----------------------------------------------------------------------------| r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 2729 Z= 0.136 Angle : 0.638 10.060 3754 Z= 0.298 Chirality : 0.043 0.153 430 Planarity : 0.007 0.051 454 Dihedral : 5.641 75.191 364 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 4.35 % Allowed : 13.44 % Favored : 82.21 % 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: 3.33 (0.46), residues: 339 helix: 2.37 (0.31), residues: 253 sheet: None (None), residues: 0 loop : 1.94 (0.79), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 79 TYR 0.005 0.001 TYR A 72 PHE 0.026 0.002 PHE B 219 TRP 0.009 0.001 TRP A 163 HIS 0.004 0.002 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 ( 2721) covalent geometry : angle 0.63235 / 0.30 ( 3748) hydrogen bonds : bond 0.03147 / 2.07 ( 184) hydrogen bonds : angle 4.05023 / 2.87 ( 552) metal coordination : bond 0.01074 / 0.74 ( 8) metal coordination : angle 2.12685 / 1.12 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.096 Fit side-chains REVERT: A 91 LEU cc_start: 0.8240 (tp) cc_final: 0.7702 (tp) REVERT: A 103 MET cc_start: 0.6934 (tpp) cc_final: 0.6669 (tpp) outliers start: 11 outliers final: 9 residues processed: 58 average time/residue: 0.0389 time to fit residues: 2.9962 Evaluate side-chains 60 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 189 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 1 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 4 optimal weight: 0.0070 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 14 optimal weight: 0.2980 chunk 30 optimal weight: 0.9990 chunk 7 optimal weight: 0.0570 chunk 13 optimal weight: 7.9990 overall best weight: 0.3716 ------------------------------------------------------------------------------- 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 = 0.4214 r_free = 0.4214 target = 0.194716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.165320 restraints weight = 4037.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.166142 restraints weight = 3405.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.166149 restraints weight = 2945.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.166149 restraints weight = 2936.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.166149 restraints weight = 2936.466| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 2729 Z= 0.134 Angle : 0.616 10.135 3754 Z= 0.288 Chirality : 0.043 0.154 430 Planarity : 0.007 0.052 454 Dihedral : 5.305 67.391 364 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 5.53 % Allowed : 13.83 % Favored : 80.63 % 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: 3.40 (0.46), residues: 339 helix: 2.43 (0.31), residues: 252 sheet: None (None), residues: 0 loop : 1.94 (0.78), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 79 TYR 0.005 0.001 TYR B 200 PHE 0.026 0.002 PHE B 219 TRP 0.009 0.001 TRP A 163 HIS 0.003 0.002 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.13 ( 2721) covalent geometry : angle 0.61123 / 0.29 ( 3748) hydrogen bonds : bond 0.02951 / 1.94 ( 184) hydrogen bonds : angle 3.86498 / 2.72 ( 552) metal coordination : bond 0.01161 / 0.73 ( 8) metal coordination : angle 1.99237 / 1.06 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 50 time to evaluate : 0.078 Fit side-chains REVERT: A 79 ARG cc_start: 0.8638 (tpp80) cc_final: 0.8300 (mtm-85) REVERT: A 91 LEU cc_start: 0.8175 (tp) cc_final: 0.7517 (tp) REVERT: A 103 MET cc_start: 0.6932 (tpp) cc_final: 0.6617 (tpp) REVERT: B 9 LEU cc_start: 0.5872 (OUTLIER) cc_final: 0.5175 (mt) REVERT: B 87 LEU cc_start: 0.8165 (mt) cc_final: 0.7936 (mt) outliers start: 14 outliers final: 7 residues processed: 55 average time/residue: 0.0355 time to fit residues: 2.5867 Evaluate side-chains 57 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 189 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 31 optimal weight: 0.7980 chunk 3 optimal weight: 0.4980 chunk 30 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.4193 r_free = 0.4193 target = 0.192198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.163015 restraints weight = 4014.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.163764 restraints weight = 3394.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 16)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.163771 restraints weight = 2990.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.163771 restraints weight = 2980.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.163771 restraints weight = 2980.913| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 2729 Z= 0.218 Angle : 0.701 9.904 3754 Z= 0.335 Chirality : 0.047 0.158 430 Planarity : 0.008 0.052 454 Dihedral : 5.293 57.971 364 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.95 % Allowed : 17.79 % Favored : 78.26 % 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: 2.98 (0.46), residues: 339 helix: 2.18 (0.32), residues: 246 sheet: None (None), residues: 0 loop : 1.63 (0.75), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 79 TYR 0.006 0.001 TYR B 100 PHE 0.026 0.002 PHE B 219 TRP 0.015 0.001 TRP B 199 HIS 0.004 0.002 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00529 / 0.22 ( 2721) covalent geometry : angle 0.69064 / 0.33 ( 3748) hydrogen bonds : bond 0.03533 / 2.37 ( 184) hydrogen bonds : angle 4.20208 / 2.96 ( 552) metal coordination : bond 0.02456 / 1.41 ( 8) metal coordination : angle 3.08329 / 1.54 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.106 Fit side-chains REVERT: B 9 LEU cc_start: 0.6105 (OUTLIER) cc_final: 0.5473 (mt) outliers start: 10 outliers final: 7 residues processed: 54 average time/residue: 0.0526 time to fit residues: 3.5909 Evaluate side-chains 57 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 189 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 14 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 0.0870 chunk 24 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 7 optimal weight: 0.0870 overall best weight: 0.4136 ------------------------------------------------------------------------------- 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 = 0.4210 r_free = 0.4210 target = 0.194259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.174280 restraints weight = 3987.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.172852 restraints weight = 9050.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.173265 restraints weight = 7639.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.173821 restraints weight = 4564.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.173463 restraints weight = 5649.657| |-----------------------------------------------------------------------------| r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6873 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 2729 Z= 0.139 Angle : 0.637 11.345 3754 Z= 0.297 Chirality : 0.043 0.156 430 Planarity : 0.007 0.053 454 Dihedral : 4.841 48.847 364 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 4.74 % Allowed : 17.39 % Favored : 77.87 % 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: 2.94 (0.47), residues: 339 helix: 2.15 (0.32), residues: 251 sheet: None (None), residues: 0 loop : 1.59 (0.78), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 79 TYR 0.004 0.001 TYR B 72 PHE 0.025 0.001 PHE B 219 TRP 0.013 0.001 TRP A 163 HIS 0.003 0.002 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 ( 2721) covalent geometry : angle 0.63326 / 0.30 ( 3748) hydrogen bonds : bond 0.03044 / 1.98 ( 184) hydrogen bonds : angle 3.96047 / 2.81 ( 552) metal coordination : bond 0.01381 / 0.83 ( 8) metal coordination : angle 1.80624 / 0.95 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 0.098 Fit side-chains REVERT: A 91 LEU cc_start: 0.8104 (tp) cc_final: 0.7522 (tp) REVERT: B 9 LEU cc_start: 0.6251 (OUTLIER) cc_final: 0.5652 (mt) REVERT: B 79 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7860 (mtt-85) outliers start: 12 outliers final: 8 residues processed: 55 average time/residue: 0.0485 time to fit residues: 3.4076 Evaluate side-chains 57 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 189 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 18 optimal weight: 1.9990 chunk 16 optimal weight: 0.0060 chunk 12 optimal weight: 0.0000 chunk 30 optimal weight: 6.9990 chunk 22 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 overall best weight: 0.3800 ------------------------------------------------------------------------------- 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 = 0.4214 r_free = 0.4214 target = 0.194643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.174563 restraints weight = 4100.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.173471 restraints weight = 8868.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.173977 restraints weight = 7231.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.174623 restraints weight = 4662.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.174735 restraints weight = 4879.903| |-----------------------------------------------------------------------------| r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6847 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 2729 Z= 0.135 Angle : 0.627 10.896 3754 Z= 0.292 Chirality : 0.043 0.155 430 Planarity : 0.007 0.054 454 Dihedral : 4.520 39.784 364 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.95 % Allowed : 18.97 % Favored : 77.08 % 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: 3.03 (0.47), residues: 339 helix: 2.23 (0.32), residues: 250 sheet: None (None), residues: 0 loop : 1.58 (0.77), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 79 TYR 0.003 0.001 TYR A 206 PHE 0.025 0.001 PHE B 219 TRP 0.012 0.001 TRP A 163 HIS 0.003 0.002 HIS B 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.13 ( 2721) covalent geometry : angle 0.62362 / 0.29 ( 3748) hydrogen bonds : bond 0.02915 / 1.89 ( 184) hydrogen bonds : angle 3.87136 / 2.74 ( 552) metal coordination : bond 0.01305 / 0.78 ( 8) metal coordination : angle 1.69811 / 0.91 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.108 Fit side-chains REVERT: A 91 LEU cc_start: 0.8165 (tp) cc_final: 0.7477 (tp) REVERT: B 9 LEU cc_start: 0.6313 (OUTLIER) cc_final: 0.5644 (mt) REVERT: B 79 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7869 (mtt-85) outliers start: 10 outliers final: 8 residues processed: 54 average time/residue: 0.0404 time to fit residues: 2.7785 Evaluate side-chains 57 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 189 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 15 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 5 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 25 optimal weight: 0.0870 chunk 19 optimal weight: 0.2980 overall best weight: 0.4558 ------------------------------------------------------------------------------- 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 = 0.4207 r_free = 0.4207 target = 0.194080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.174904 restraints weight = 4188.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.173778 restraints weight = 8526.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.174445 restraints weight = 6948.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.175430 restraints weight = 4375.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.174271 restraints weight = 4756.406| |-----------------------------------------------------------------------------| r_work (final): 0.3998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 2729 Z= 0.145 Angle : 0.640 10.970 3754 Z= 0.297 Chirality : 0.043 0.156 430 Planarity : 0.007 0.055 454 Dihedral : 4.430 35.409 364 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.95 % Allowed : 18.58 % Favored : 77.47 % 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: 3.05 (0.47), residues: 339 helix: 2.25 (0.32), residues: 250 sheet: None (None), residues: 0 loop : 1.57 (0.77), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 79 TYR 0.003 0.001 TYR B 72 PHE 0.025 0.001 PHE B 219 TRP 0.011 0.001 TRP A 163 HIS 0.003 0.001 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.14 ( 2721) covalent geometry : angle 0.63715 / 0.30 ( 3748) hydrogen bonds : bond 0.02927 / 1.90 ( 184) hydrogen bonds : angle 3.84937 / 2.71 ( 552) metal coordination : bond 0.01477 / 0.85 ( 8) metal coordination : angle 1.66276 / 0.88 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.099 Fit side-chains REVERT: A 30 GLN cc_start: 0.8413 (tt0) cc_final: 0.8178 (tt0) REVERT: A 91 LEU cc_start: 0.8135 (tp) cc_final: 0.7628 (tp) REVERT: B 9 LEU cc_start: 0.6352 (OUTLIER) cc_final: 0.5698 (mt) REVERT: B 79 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.7861 (mtt-85) outliers start: 10 outliers final: 8 residues processed: 53 average time/residue: 0.0490 time to fit residues: 3.2887 Evaluate side-chains 56 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 189 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 33 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 3 optimal weight: 0.3980 chunk 2 optimal weight: 0.3980 chunk 21 optimal weight: 0.2980 chunk 4 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.4205 r_free = 0.4205 target = 0.193814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.173950 restraints weight = 4162.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.172416 restraints weight = 8685.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.173507 restraints weight = 6628.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.173637 restraints weight = 4138.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.173869 restraints weight = 4055.323| |-----------------------------------------------------------------------------| r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 2729 Z= 0.145 Angle : 0.634 10.772 3754 Z= 0.296 Chirality : 0.043 0.157 430 Planarity : 0.008 0.061 454 Dihedral : 4.246 28.066 364 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.56 % Allowed : 19.37 % Favored : 77.08 % 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: 3.00 (0.47), residues: 339 helix: 2.23 (0.32), residues: 250 sheet: None (None), residues: 0 loop : 1.52 (0.78), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 79 TYR 0.004 0.001 TYR B 200 PHE 0.025 0.001 PHE B 219 TRP 0.011 0.001 TRP A 163 HIS 0.003 0.002 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.14 ( 2721) covalent geometry : angle 0.63132 / 0.30 ( 3748) hydrogen bonds : bond 0.02916 / 1.91 ( 184) hydrogen bonds : angle 3.81019 / 2.69 ( 552) metal coordination : bond 0.01448 / 0.81 ( 8) metal coordination : angle 1.65373 / 0.87 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.097 Fit side-chains REVERT: A 91 LEU cc_start: 0.8137 (tp) cc_final: 0.7450 (tp) REVERT: B 9 LEU cc_start: 0.6382 (OUTLIER) cc_final: 0.5728 (mt) outliers start: 9 outliers final: 7 residues processed: 54 average time/residue: 0.0479 time to fit residues: 3.2820 Evaluate side-chains 57 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 189 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 3 optimal weight: 0.1980 chunk 25 optimal weight: 0.8980 chunk 32 optimal weight: 0.0970 chunk 17 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 33 optimal weight: 0.2980 chunk 23 optimal weight: 0.1980 overall best weight: 0.3378 ------------------------------------------------------------------------------- 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 = 0.4218 r_free = 0.4218 target = 0.195215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.166951 restraints weight = 4099.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.167791 restraints weight = 3378.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.168342 restraints weight = 2909.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.168683 restraints weight = 2605.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.169326 restraints weight = 2491.907| |-----------------------------------------------------------------------------| r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 2729 Z= 0.126 Angle : 0.631 10.857 3754 Z= 0.289 Chirality : 0.042 0.155 430 Planarity : 0.007 0.056 454 Dihedral : 4.045 22.799 364 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.16 % Allowed : 18.97 % Favored : 77.87 % 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: 3.06 (0.47), residues: 339 helix: 2.26 (0.32), residues: 250 sheet: None (None), residues: 0 loop : 1.56 (0.78), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 79 TYR 0.003 0.001 TYR B 200 PHE 0.025 0.001 PHE B 219 TRP 0.011 0.001 TRP A 163 HIS 0.003 0.002 HIS B 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 2721) covalent geometry : angle 0.62918 / 0.29 ( 3748) hydrogen bonds : bond 0.02773 / 1.79 ( 184) hydrogen bonds : angle 3.72174 / 2.63 ( 552) metal coordination : bond 0.01124 / 0.63 ( 8) metal coordination : angle 1.30704 / 0.72 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 783.70 seconds wall clock time: 14 minutes 5.95 seconds (845.95 seconds total)