Starting phenix.real_space_refine on Fri May 9 14:43:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iyx_61003/05_2025/9iyx_61003.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iyx_61003/05_2025/9iyx_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9iyx_61003/05_2025/9iyx_61003.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iyx_61003/05_2025/9iyx_61003.map" model { file = "/net/cci-nas-00/data/ceres_data/9iyx_61003/05_2025/9iyx_61003.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iyx_61003/05_2025/9iyx_61003.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'PHE:plan': 5, 'GLN:plan1': 1, 'ASN:plan1': 2, 'TRP:plan': 4, '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, 'PHE:plan': 2, 'TRP:plan': 3, '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: 2.59, per 1000 atoms: 0.99 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: 0.83 Conformation dependent library (CDL) restraints added in 338.5 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: 0.24 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: 0.60 Time building geometry restraints manager: 0.90 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 226 or resid 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: 1.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.380 Find NCS groups from input model: 0.120 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6669 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 : 11.46 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.013 0.001 TRP B 36 HIS 0.004 0.002 HIS A 60 PHE 0.018 0.002 PHE B 219 TYR 0.008 0.001 TYR B 200 ARG 0.002 0.001 ARG A 73 Details of bonding type rmsd hydrogen bonds : bond 0.17505 ( 184) hydrogen bonds : angle 7.90669 ( 552) metal coordination : bond 0.01410 ( 8) metal coordination : angle 3.35346 ( 6) covalent geometry : bond 0.00449 ( 2721) covalent geometry : angle 0.78017 ( 3748) *********************** 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 : 0.293 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: 0.1279 time to fit residues: 9.4891 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 : 0.290 ------------------------------------------------------------------------------- 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 28 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 14 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 chunk 17 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 0.1980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4221 r_free = 0.4221 target = 0.194770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.164685 restraints weight = 4003.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.165250 restraints weight = 3366.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.165319 restraints weight = 3068.632| |-----------------------------------------------------------------------------| r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 2729 Z= 0.203 Angle : 0.722 7.375 3754 Z= 0.350 Chirality : 0.047 0.155 430 Planarity : 0.008 0.054 454 Dihedral : 6.129 78.693 366 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.37 % Allowed : 10.28 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.89 (0.46), residues: 339 helix: 2.02 (0.31), residues: 252 sheet: None (None), residues: 0 loop : 1.88 (0.81), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 163 HIS 0.004 0.002 HIS A 60 PHE 0.023 0.002 PHE B 170 TYR 0.013 0.002 TYR B 200 ARG 0.003 0.001 ARG B 73 Details of bonding type rmsd hydrogen bonds : bond 0.04135 ( 184) hydrogen bonds : angle 4.84973 ( 552) metal coordination : bond 0.01559 ( 8) metal coordination : angle 3.09262 ( 6) covalent geometry : bond 0.00486 ( 2721) covalent geometry : angle 0.71189 ( 3748) *********************** 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 : 0.278 Fit side-chains REVERT: A 103 MET cc_start: 0.7151 (tpp) cc_final: 0.6798 (tpp) outliers start: 6 outliers final: 2 residues processed: 57 average time/residue: 0.0984 time to fit residues: 7.2164 Evaluate side-chains 51 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.273 ------------------------------------------------------------------------------- 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 23 optimal weight: 0.1980 chunk 19 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 4 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 13 optimal weight: 0.4980 chunk 15 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4202 r_free = 0.4202 target = 0.192911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.163602 restraints weight = 4062.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.164642 restraints weight = 3399.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.164489 restraints weight = 2920.112| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 2729 Z= 0.181 Angle : 0.676 6.979 3754 Z= 0.327 Chirality : 0.045 0.154 430 Planarity : 0.008 0.054 454 Dihedral : 5.941 76.914 364 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.56 % Allowed : 15.42 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.89 (0.46), residues: 339 helix: 2.12 (0.32), residues: 252 sheet: None (None), residues: 0 loop : 1.52 (0.78), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 163 HIS 0.004 0.002 HIS A 60 PHE 0.024 0.002 PHE B 219 TYR 0.009 0.001 TYR B 200 ARG 0.002 0.000 ARG B 79 Details of bonding type rmsd hydrogen bonds : bond 0.03749 ( 184) hydrogen bonds : angle 4.39657 ( 552) metal coordination : bond 0.01665 ( 8) metal coordination : angle 3.03806 ( 6) covalent geometry : bond 0.00434 ( 2721) covalent geometry : angle 0.66535 ( 3748) *********************** 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: 9 poor density : 50 time to evaluate : 0.271 Fit side-chains REVERT: A 103 MET cc_start: 0.7064 (tpp) cc_final: 0.6651 (tpp) outliers start: 9 outliers final: 5 residues processed: 54 average time/residue: 0.0885 time to fit residues: 6.3033 Evaluate side-chains 55 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 69 CYS Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain B residue 39 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 16 optimal weight: 0.0980 chunk 29 optimal weight: 0.3980 chunk 14 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 13 optimal weight: 8.9990 chunk 27 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 23 optimal weight: 0.2980 chunk 18 optimal weight: 0.9980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.193373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.164420 restraints weight = 4123.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.164994 restraints weight = 3441.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.165313 restraints weight = 3028.847| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 moved from start: 0.2614 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= 0.141 Angle : 0.637 10.845 3754 Z= 0.301 Chirality : 0.043 0.154 430 Planarity : 0.007 0.052 454 Dihedral : 5.653 73.243 364 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 5.14 % Allowed : 15.02 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.05 (0.46), residues: 339 helix: 2.24 (0.32), residues: 252 sheet: None (None), residues: 0 loop : 1.56 (0.78), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 163 HIS 0.003 0.002 HIS A 60 PHE 0.025 0.002 PHE B 219 TYR 0.004 0.001 TYR B 200 ARG 0.002 0.000 ARG A 73 Details of bonding type rmsd hydrogen bonds : bond 0.03187 ( 184) hydrogen bonds : angle 4.09849 ( 552) metal coordination : bond 0.01312 ( 8) metal coordination : angle 2.27110 ( 6) covalent geometry : bond 0.00340 ( 2721) covalent geometry : angle 0.63084 ( 3748) *********************** 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 62 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 0.291 Fit side-chains REVERT: A 91 LEU cc_start: 0.8186 (tp) cc_final: 0.7655 (tp) REVERT: A 103 MET cc_start: 0.7014 (tpp) cc_final: 0.6645 (tpp) outliers start: 13 outliers final: 8 residues processed: 54 average time/residue: 0.0890 time to fit residues: 6.3191 Evaluate side-chains 55 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.281 ------------------------------------------------------------------------------- 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 97 LEU Chi-restraints excluded: chain B residue 9 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 7 optimal weight: 0.0980 chunk 2 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 29 optimal weight: 0.0980 chunk 18 optimal weight: 0.8980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.192455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.162861 restraints weight = 4099.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.163711 restraints weight = 3439.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.163878 restraints weight = 2983.014| |-----------------------------------------------------------------------------| r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 2729 Z= 0.152 Angle : 0.632 10.328 3754 Z= 0.299 Chirality : 0.043 0.154 430 Planarity : 0.007 0.052 454 Dihedral : 5.385 66.028 364 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 4.35 % Allowed : 17.79 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.09 (0.46), residues: 339 helix: 2.27 (0.32), residues: 252 sheet: None (None), residues: 0 loop : 1.58 (0.78), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 163 HIS 0.003 0.002 HIS A 60 PHE 0.025 0.002 PHE B 219 TYR 0.004 0.001 TYR A 206 ARG 0.002 0.000 ARG B 79 Details of bonding type rmsd hydrogen bonds : bond 0.03139 ( 184) hydrogen bonds : angle 4.01519 ( 552) metal coordination : bond 0.01549 ( 8) metal coordination : angle 2.03539 ( 6) covalent geometry : bond 0.00370 ( 2721) covalent geometry : angle 0.62689 ( 3748) *********************** 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 59 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: A 91 LEU cc_start: 0.8212 (tp) cc_final: 0.7621 (tp) REVERT: A 103 MET cc_start: 0.6876 (tpp) cc_final: 0.6540 (tpp) REVERT: B 9 LEU cc_start: 0.5773 (OUTLIER) cc_final: 0.4989 (mt) REVERT: B 87 LEU cc_start: 0.8184 (mt) cc_final: 0.7939 (mt) outliers start: 11 outliers final: 8 residues processed: 54 average time/residue: 0.1108 time to fit residues: 7.5435 Evaluate side-chains 55 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.281 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 14 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 4 optimal weight: 0.1980 chunk 26 optimal weight: 0.6980 chunk 21 optimal weight: 0.0570 chunk 6 optimal weight: 0.5980 chunk 29 optimal weight: 0.0470 chunk 18 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 overall best weight: 0.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.195227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.176018 restraints weight = 4122.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.174849 restraints weight = 8463.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.175404 restraints weight = 7000.589| |-----------------------------------------------------------------------------| r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6755 moved from start: 0.3075 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= 0.126 Angle : 0.601 10.111 3754 Z= 0.282 Chirality : 0.042 0.155 430 Planarity : 0.007 0.053 454 Dihedral : 4.933 55.473 364 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.56 % Allowed : 18.97 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.38 (0.46), residues: 339 helix: 2.52 (0.32), residues: 246 sheet: None (None), residues: 0 loop : 1.65 (0.75), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 163 HIS 0.002 0.002 HIS B 60 PHE 0.025 0.001 PHE B 219 TYR 0.003 0.001 TYR B 72 ARG 0.003 0.001 ARG A 78 Details of bonding type rmsd hydrogen bonds : bond 0.02882 ( 184) hydrogen bonds : angle 3.82602 ( 552) metal coordination : bond 0.01097 ( 8) metal coordination : angle 1.70145 ( 6) covalent geometry : bond 0.00304 ( 2721) covalent geometry : angle 0.59713 ( 3748) *********************** 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 58 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.296 Fit side-chains REVERT: A 91 LEU cc_start: 0.8195 (tp) cc_final: 0.7485 (tp) REVERT: B 9 LEU cc_start: 0.6100 (OUTLIER) cc_final: 0.5199 (mt) REVERT: B 75 MET cc_start: 0.8746 (ttp) cc_final: 0.8545 (ttt) outliers start: 9 outliers final: 6 residues processed: 54 average time/residue: 0.0962 time to fit residues: 6.8048 Evaluate side-chains 54 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.295 ------------------------------------------------------------------------------- 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 39 LEU 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 23 optimal weight: 0.2980 chunk 10 optimal weight: 0.0970 chunk 1 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 5 optimal weight: 0.2980 chunk 18 optimal weight: 2.9990 chunk 6 optimal weight: 0.2980 chunk 20 optimal weight: 0.0070 overall best weight: 0.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.198549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.168628 restraints weight = 4128.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.169812 restraints weight = 3104.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.170780 restraints weight = 2611.608| |-----------------------------------------------------------------------------| r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6925 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2729 Z= 0.111 Angle : 0.606 10.873 3754 Z= 0.278 Chirality : 0.041 0.153 430 Planarity : 0.007 0.054 454 Dihedral : 4.345 40.332 364 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.95 % Allowed : 19.76 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.20 (0.46), residues: 339 helix: 2.31 (0.32), residues: 257 sheet: None (None), residues: 0 loop : 1.70 (0.81), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 36 HIS 0.002 0.001 HIS B 60 PHE 0.025 0.001 PHE B 219 TYR 0.003 0.000 TYR B 72 ARG 0.002 0.000 ARG A 78 Details of bonding type rmsd hydrogen bonds : bond 0.02662 ( 184) hydrogen bonds : angle 3.70371 ( 552) metal coordination : bond 0.00736 ( 8) metal coordination : angle 1.40911 ( 6) covalent geometry : bond 0.00265 ( 2721) covalent geometry : angle 0.60401 ( 3748) *********************** 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 60 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.261 Fit side-chains REVERT: A 91 LEU cc_start: 0.8088 (tp) cc_final: 0.7420 (tp) REVERT: B 9 LEU cc_start: 0.5590 (OUTLIER) cc_final: 0.4956 (mt) REVERT: B 75 MET cc_start: 0.8742 (ttp) cc_final: 0.8442 (ttt) REVERT: B 79 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.7552 (mmt90) outliers start: 10 outliers final: 7 residues processed: 55 average time/residue: 0.1234 time to fit residues: 8.3833 Evaluate side-chains 56 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.289 ------------------------------------------------------------------------------- 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 39 LEU Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 92 ILE 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 31 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 22 optimal weight: 0.4980 chunk 23 optimal weight: 0.2980 chunk 33 optimal weight: 0.6980 chunk 6 optimal weight: 0.4980 chunk 8 optimal weight: 0.9980 chunk 19 optimal weight: 0.0980 chunk 3 optimal weight: 0.4980 chunk 12 optimal weight: 5.9990 chunk 32 optimal weight: 0.4980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.195392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.166940 restraints weight = 4095.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.167774 restraints weight = 3341.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.167931 restraints weight = 2925.035| |-----------------------------------------------------------------------------| r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.3362 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= 0.130 Angle : 0.615 10.770 3754 Z= 0.284 Chirality : 0.042 0.154 430 Planarity : 0.007 0.054 454 Dihedral : 4.299 37.073 364 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.95 % Allowed : 19.37 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.22 (0.47), residues: 339 helix: 2.36 (0.32), residues: 251 sheet: None (None), residues: 0 loop : 1.68 (0.78), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 163 HIS 0.003 0.001 HIS A 60 PHE 0.026 0.001 PHE B 219 TYR 0.003 0.001 TYR A 72 ARG 0.003 0.001 ARG A 78 Details of bonding type rmsd hydrogen bonds : bond 0.02755 ( 184) hydrogen bonds : angle 3.73797 ( 552) metal coordination : bond 0.01220 ( 8) metal coordination : angle 1.56730 ( 6) covalent geometry : bond 0.00316 ( 2721) covalent geometry : angle 0.61269 ( 3748) *********************** 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 57 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.292 Fit side-chains REVERT: A 91 LEU cc_start: 0.8136 (tp) cc_final: 0.7429 (tp) REVERT: B 9 LEU cc_start: 0.5876 (OUTLIER) cc_final: 0.5259 (mt) REVERT: B 75 MET cc_start: 0.8775 (ttp) cc_final: 0.8464 (ttt) REVERT: B 79 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.7609 (mmt90) outliers start: 10 outliers final: 8 residues processed: 53 average time/residue: 0.1186 time to fit residues: 7.8999 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 : 0.315 ------------------------------------------------------------------------------- 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 92 ILE 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 18 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 20 optimal weight: 0.0270 chunk 25 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 26 optimal weight: 0.2980 chunk 14 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.193911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.164750 restraints weight = 4117.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.165732 restraints weight = 3346.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.165732 restraints weight = 2887.858| |-----------------------------------------------------------------------------| r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.3485 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= 0.140 Angle : 0.626 10.952 3754 Z= 0.290 Chirality : 0.043 0.157 430 Planarity : 0.007 0.055 454 Dihedral : 4.196 29.315 364 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.56 % Allowed : 20.95 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.19 (0.47), residues: 339 helix: 2.34 (0.32), residues: 251 sheet: None (None), residues: 0 loop : 1.64 (0.78), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 163 HIS 0.003 0.001 HIS A 60 PHE 0.026 0.001 PHE B 219 TYR 0.004 0.001 TYR B 72 ARG 0.003 0.001 ARG A 78 Details of bonding type rmsd hydrogen bonds : bond 0.02875 ( 184) hydrogen bonds : angle 3.75048 ( 552) metal coordination : bond 0.01480 ( 8) metal coordination : angle 1.60872 ( 6) covalent geometry : bond 0.00344 ( 2721) covalent geometry : angle 0.62367 ( 3748) *********************** 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 58 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.266 Fit side-chains REVERT: B 9 LEU cc_start: 0.5971 (OUTLIER) cc_final: 0.5398 (mt) REVERT: B 30 GLN cc_start: 0.7766 (tp40) cc_final: 0.7196 (tt0) outliers start: 9 outliers final: 7 residues processed: 55 average time/residue: 0.1254 time to fit residues: 8.4809 Evaluate side-chains 55 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.308 ------------------------------------------------------------------------------- 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 92 ILE 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 5 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 1 optimal weight: 0.3980 chunk 31 optimal weight: 0.0970 chunk 23 optimal weight: 0.1980 chunk 22 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 32 optimal weight: 0.0040 overall best weight: 0.2990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.195956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.167940 restraints weight = 4062.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.168632 restraints weight = 3201.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.168632 restraints weight = 2877.514| |-----------------------------------------------------------------------------| r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.3613 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= 0.122 Angle : 0.628 10.855 3754 Z= 0.287 Chirality : 0.042 0.154 430 Planarity : 0.007 0.055 454 Dihedral : 4.013 24.505 364 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.16 % Allowed : 21.74 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.18 (0.47), residues: 339 helix: 2.34 (0.32), residues: 250 sheet: None (None), residues: 0 loop : 1.65 (0.77), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 163 HIS 0.002 0.002 HIS B 60 PHE 0.026 0.001 PHE B 219 TYR 0.003 0.000 TYR A 206 ARG 0.004 0.001 ARG A 78 Details of bonding type rmsd hydrogen bonds : bond 0.02736 ( 184) hydrogen bonds : angle 3.68116 ( 552) metal coordination : bond 0.01059 ( 8) metal coordination : angle 1.37320 ( 6) covalent geometry : bond 0.00298 ( 2721) covalent geometry : angle 0.62616 ( 3748) ********************** 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: 8 poor density : 49 time to evaluate : 0.285 Fit side-chains REVERT: A 91 LEU cc_start: 0.8074 (tp) cc_final: 0.7423 (tp) REVERT: B 9 LEU cc_start: 0.6030 (OUTLIER) cc_final: 0.5411 (mt) outliers start: 8 outliers final: 7 residues processed: 54 average time/residue: 0.1268 time to fit residues: 8.4772 Evaluate side-chains 55 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.304 ------------------------------------------------------------------------------- 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 92 ILE 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 7 optimal weight: 0.0980 chunk 11 optimal weight: 0.7980 chunk 13 optimal weight: 0.0020 chunk 23 optimal weight: 0.2980 chunk 17 optimal weight: 0.0970 chunk 27 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 31 optimal weight: 0.1980 chunk 19 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 overall best weight: 0.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.197762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.170376 restraints weight = 4083.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.171231 restraints weight = 3464.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.171702 restraints weight = 3090.254| |-----------------------------------------------------------------------------| r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2729 Z= 0.106 Angle : 0.605 10.686 3754 Z= 0.277 Chirality : 0.041 0.151 430 Planarity : 0.007 0.054 454 Dihedral : 3.763 17.244 364 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.95 % Allowed : 20.95 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.30 (0.46), residues: 339 helix: 2.40 (0.32), residues: 250 sheet: None (None), residues: 0 loop : 1.77 (0.78), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 36 HIS 0.003 0.002 HIS B 60 PHE 0.026 0.001 PHE B 219 TYR 0.004 0.001 TYR A 206 ARG 0.005 0.001 ARG A 78 Details of bonding type rmsd hydrogen bonds : bond 0.02545 ( 184) hydrogen bonds : angle 3.57402 ( 552) metal coordination : bond 0.00525 ( 8) metal coordination : angle 1.22828 ( 6) covalent geometry : bond 0.00250 ( 2721) covalent geometry : angle 0.60370 ( 3748) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1423.12 seconds wall clock time: 25 minutes 22.22 seconds (1522.22 seconds total)