Starting phenix.real_space_refine on Mon Feb 10 21:12:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iyx_61003/02_2025/9iyx_61003.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iyx_61003/02_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_61003/02_2025/9iyx_61003.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iyx_61003/02_2025/9iyx_61003.map" model { file = "/net/cci-nas-00/data/ceres_data/9iyx_61003/02_2025/9iyx_61003.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iyx_61003/02_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-5592/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: 2.46, per 1000 atoms: 0.94 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: 0.70 Conformation dependent library (CDL) restraints added in 309.6 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: 0.27 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: 0.68 Time building geometry restraints manager: 0.79 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: 1.660 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: 0.010 Set scattering table: 0.030 Process input model: 12.010 Find NCS groups from input model: 0.130 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: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.740 ------------------------------------------------------------------------------- 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 : 0.004 0.058 2721 Z= 0.278 Angle : 0.780 10.952 3748 Z= 0.472 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 *********************** 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 : 0.322 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: 0.1370 time to fit residues: 10.1340 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 : 0.312 ------------------------------------------------------------------------------- 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 2721 Z= 0.326 Angle : 0.712 7.375 3748 Z= 0.349 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 *********************** 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 : 0.224 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: 0.0932 time to fit residues: 6.8269 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 : 0.268 ------------------------------------------------------------------------------- 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: 0.9980 chunk 10 optimal weight: 4.9990 chunk 21 optimal weight: 0.4980 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: 0.1980 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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 = 0.4223 r_free = 0.4223 target = 0.195053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.164397 restraints weight = 4062.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.165637 restraints weight = 3219.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.166088 restraints weight = 2740.391| |-----------------------------------------------------------------------------| r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6951 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 2721 Z= 0.240 Angle : 0.638 7.299 3748 Z= 0.309 Chirality : 0.044 0.153 430 Planarity : 0.008 0.053 454 Dihedral : 5.874 77.574 364 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.77 % Allowed : 15.42 % Favored : 81.82 % 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: 3.06 (0.46), residues: 339 helix: 2.24 (0.32), residues: 252 sheet: None (None), residues: 0 loop : 1.63 (0.78), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 163 HIS 0.004 0.002 HIS A 60 PHE 0.024 0.002 PHE B 219 TYR 0.007 0.001 TYR B 200 ARG 0.002 0.000 ARG A 73 *********************** 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 56 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.279 Fit side-chains REVERT: A 103 MET cc_start: 0.7041 (tpp) cc_final: 0.6672 (tpp) outliers start: 7 outliers final: 4 residues processed: 52 average time/residue: 0.0952 time to fit residues: 6.5121 Evaluate side-chains 51 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR 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: 0.0060 chunk 29 optimal weight: 0.0980 chunk 14 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 20 optimal weight: 0.0020 chunk 31 optimal weight: 0.2980 chunk 24 optimal weight: 0.5980 chunk 23 optimal weight: 0.3980 chunk 18 optimal weight: 0.9990 overall best weight: 0.1604 ------------------------------------------------------------------------------- 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 = 0.4250 r_free = 0.4250 target = 0.198294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.170080 restraints weight = 4068.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.170954 restraints weight = 3320.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.170954 restraints weight = 2914.303| |-----------------------------------------------------------------------------| r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2721 Z= 0.182 Angle : 0.618 10.559 3748 Z= 0.287 Chirality : 0.042 0.153 430 Planarity : 0.007 0.052 454 Dihedral : 5.533 74.085 364 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 4.35 % Allowed : 15.02 % 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 (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: 2.38 (0.31), residues: 253 sheet: None (None), residues: 0 loop : 1.83 (0.78), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 163 HIS 0.003 0.002 HIS A 60 PHE 0.026 0.002 PHE B 219 TYR 0.005 0.001 TYR B 200 ARG 0.003 0.001 ARG A 73 *********************** 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: 11 poor density : 51 time to evaluate : 0.306 Fit side-chains REVERT: A 79 ARG cc_start: 0.8578 (tpp80) cc_final: 0.8276 (mtm-85) REVERT: A 91 LEU cc_start: 0.8101 (tp) cc_final: 0.7471 (tp) REVERT: A 103 MET cc_start: 0.6929 (tpp) cc_final: 0.6681 (tpp) REVERT: B 59 ASN cc_start: 0.6987 (t0) cc_final: 0.6756 (t0) outliers start: 11 outliers final: 8 residues processed: 55 average time/residue: 0.0956 time to fit residues: 6.9374 Evaluate side-chains 58 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.299 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 2 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 20 optimal weight: 0.1980 chunk 29 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4209 r_free = 0.4209 target = 0.194049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.164852 restraints weight = 4059.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.165443 restraints weight = 3433.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.165490 restraints weight = 3037.049| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 2721 Z= 0.289 Angle : 0.654 9.898 3748 Z= 0.312 Chirality : 0.044 0.155 430 Planarity : 0.008 0.053 454 Dihedral : 5.411 66.902 364 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.56 % Allowed : 18.58 % 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: 3.10 (0.46), residues: 339 helix: 2.22 (0.32), residues: 252 sheet: None (None), residues: 0 loop : 1.80 (0.78), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 199 HIS 0.005 0.002 HIS A 60 PHE 0.026 0.002 PHE B 219 TYR 0.005 0.001 TYR B 200 ARG 0.004 0.001 ARG B 79 *********************** 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 60 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.278 Fit side-chains REVERT: A 91 LEU cc_start: 0.8301 (tp) cc_final: 0.7701 (tp) REVERT: A 103 MET cc_start: 0.6961 (tpp) cc_final: 0.6609 (tpp) REVERT: B 9 LEU cc_start: 0.5894 (OUTLIER) cc_final: 0.5214 (mt) REVERT: B 79 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.8105 (mtp85) outliers start: 9 outliers final: 5 residues processed: 56 average time/residue: 0.1182 time to fit residues: 8.3897 Evaluate side-chains 56 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.318 ------------------------------------------------------------------------------- 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 189 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 14 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 4 optimal weight: 0.2980 chunk 26 optimal weight: 0.9990 chunk 21 optimal weight: 0.0020 chunk 6 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 16 optimal weight: 0.0970 chunk 11 optimal weight: 0.6980 overall best weight: 0.3386 ------------------------------------------------------------------------------- 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 = 0.4209 r_free = 0.4209 target = 0.194329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.165376 restraints weight = 4081.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.166349 restraints weight = 3308.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.166586 restraints weight = 2917.398| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 2721 Z= 0.209 Angle : 0.609 10.270 3748 Z= 0.284 Chirality : 0.042 0.155 430 Planarity : 0.007 0.054 454 Dihedral : 4.928 56.455 364 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 4.35 % Allowed : 18.97 % 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: 3.13 (0.47), residues: 339 helix: 2.26 (0.32), residues: 257 sheet: None (None), residues: 0 loop : 1.71 (0.81), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 163 HIS 0.003 0.002 HIS B 60 PHE 0.025 0.001 PHE B 219 TYR 0.004 0.001 TYR A 206 ARG 0.003 0.001 ARG B 79 *********************** 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 62 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.269 Fit side-chains REVERT: A 79 ARG cc_start: 0.8645 (tpp80) cc_final: 0.8286 (mtm-85) REVERT: A 91 LEU cc_start: 0.8163 (tp) cc_final: 0.7469 (tp) REVERT: A 103 MET cc_start: 0.6864 (tpp) cc_final: 0.6546 (tpp) REVERT: B 9 LEU cc_start: 0.6053 (OUTLIER) cc_final: 0.5405 (mt) outliers start: 11 outliers final: 8 residues processed: 55 average time/residue: 0.0910 time to fit residues: 6.5871 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 : 0.284 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 23 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 19 optimal weight: 0.2980 chunk 21 optimal weight: 0.4980 chunk 24 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 5 optimal weight: 0.0970 chunk 18 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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 = 0.4212 r_free = 0.4212 target = 0.194645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.175009 restraints weight = 4147.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.173941 restraints weight = 8264.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.174436 restraints weight = 7350.863| |-----------------------------------------------------------------------------| r_work (final): 0.3974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6772 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 2721 Z= 0.235 Angle : 0.628 11.231 3748 Z= 0.291 Chirality : 0.043 0.155 430 Planarity : 0.007 0.053 454 Dihedral : 4.643 46.948 364 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 4.35 % Allowed : 19.76 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.08 (0.47), residues: 339 helix: 2.22 (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 0.010 0.001 TRP A 163 HIS 0.003 0.002 HIS A 60 PHE 0.025 0.001 PHE B 219 TYR 0.004 0.001 TYR A 206 ARG 0.003 0.000 ARG B 79 *********************** 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: 11 poor density : 50 time to evaluate : 0.277 Fit side-chains REVERT: A 91 LEU cc_start: 0.8226 (tp) cc_final: 0.7677 (tp) REVERT: B 9 LEU cc_start: 0.6074 (OUTLIER) cc_final: 0.5486 (mt) REVERT: B 79 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7912 (mtt90) outliers start: 11 outliers final: 8 residues processed: 55 average time/residue: 0.1172 time to fit residues: 8.0632 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 : 0.307 ------------------------------------------------------------------------------- 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 31 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 22 optimal weight: 0.1980 chunk 23 optimal weight: 0.2980 chunk 33 optimal weight: 0.8980 chunk 6 optimal weight: 0.4980 chunk 8 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 3 optimal weight: 0.4980 chunk 12 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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 = 0.4225 r_free = 0.4225 target = 0.195784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.165805 restraints weight = 4060.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.167207 restraints weight = 3098.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.167207 restraints weight = 2644.241| |-----------------------------------------------------------------------------| r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 2721 Z= 0.224 Angle : 0.633 11.270 3748 Z= 0.291 Chirality : 0.043 0.156 430 Planarity : 0.007 0.054 454 Dihedral : 4.307 34.744 364 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % 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: 3.17 (0.47), residues: 339 helix: 2.29 (0.32), residues: 250 sheet: None (None), residues: 0 loop : 1.75 (0.78), residues: 89 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 B 79 *********************** 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 60 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.340 Fit side-chains REVERT: A 91 LEU cc_start: 0.8171 (tp) cc_final: 0.7459 (tp) REVERT: B 9 LEU cc_start: 0.6179 (OUTLIER) cc_final: 0.5522 (mt) REVERT: B 79 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7837 (mtt-85) outliers start: 10 outliers final: 8 residues processed: 55 average time/residue: 0.1191 time to fit residues: 8.2165 Evaluate side-chains 58 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.280 ------------------------------------------------------------------------------- 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 18 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 26 optimal weight: 0.4980 chunk 14 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4175 r_free = 0.4175 target = 0.190894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.170683 restraints weight = 4124.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.169642 restraints weight = 8407.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.170222 restraints weight = 7386.015| |-----------------------------------------------------------------------------| r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 2721 Z= 0.336 Angle : 0.676 10.880 3748 Z= 0.323 Chirality : 0.046 0.163 430 Planarity : 0.008 0.054 454 Dihedral : 4.591 32.886 364 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 4.35 % Allowed : 19.37 % 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: 2.70 (0.47), residues: 339 helix: 1.97 (0.32), residues: 251 sheet: None (None), residues: 0 loop : 1.50 (0.79), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 199 HIS 0.003 0.002 HIS A 60 PHE 0.026 0.002 PHE B 219 TYR 0.006 0.001 TYR B 100 ARG 0.004 0.001 ARG B 79 *********************** 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 64 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.306 Fit side-chains REVERT: B 9 LEU cc_start: 0.6344 (OUTLIER) cc_final: 0.5704 (mt) REVERT: B 30 GLN cc_start: 0.7999 (tp40) cc_final: 0.7657 (tt0) outliers start: 11 outliers final: 9 residues processed: 60 average time/residue: 0.1159 time to fit residues: 8.7785 Evaluate side-chains 61 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR 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 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 5 optimal weight: 0.4980 chunk 26 optimal weight: 0.0570 chunk 1 optimal weight: 0.4980 chunk 31 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 22 optimal weight: 0.0980 chunk 18 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 overall best weight: 0.3498 ------------------------------------------------------------------------------- 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 = 0.192872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.163838 restraints weight = 4077.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.164624 restraints weight = 3403.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.164846 restraints weight = 2952.589| |-----------------------------------------------------------------------------| r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 2721 Z= 0.215 Angle : 0.634 11.105 3748 Z= 0.297 Chirality : 0.043 0.156 430 Planarity : 0.007 0.055 454 Dihedral : 4.263 27.107 364 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % 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: 2.88 (0.47), residues: 339 helix: 2.12 (0.32), residues: 250 sheet: None (None), residues: 0 loop : 1.53 (0.78), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 163 HIS 0.003 0.002 HIS B 60 PHE 0.035 0.002 PHE B 93 TYR 0.004 0.001 TYR B 72 ARG 0.003 0.001 ARG B 79 ********************** 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 55 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.340 Fit side-chains REVERT: A 79 ARG cc_start: 0.8751 (tpp80) cc_final: 0.8475 (mmm-85) REVERT: A 91 LEU cc_start: 0.8128 (tp) cc_final: 0.7448 (tp) REVERT: B 9 LEU cc_start: 0.6275 (OUTLIER) cc_final: 0.5624 (mt) outliers start: 8 outliers final: 7 residues processed: 51 average time/residue: 0.0974 time to fit residues: 6.5154 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 : 0.328 ------------------------------------------------------------------------------- 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 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 7 optimal weight: 0.2980 chunk 11 optimal weight: 0.5980 chunk 13 optimal weight: 0.1980 chunk 23 optimal weight: 0.9980 chunk 17 optimal weight: 0.0050 chunk 27 optimal weight: 0.5980 chunk 5 optimal weight: 0.0570 chunk 31 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 10 optimal weight: 0.0060 chunk 26 optimal weight: 0.3980 overall best weight: 0.1128 ------------------------------------------------------------------------------- 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 = 0.4229 r_free = 0.4229 target = 0.196653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.168169 restraints weight = 4080.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.168697 restraints weight = 3206.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.169790 restraints weight = 2869.419| |-----------------------------------------------------------------------------| r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 2721 Z= 0.162 Angle : 0.591 10.684 3748 Z= 0.275 Chirality : 0.041 0.149 430 Planarity : 0.007 0.056 454 Dihedral : 3.782 17.766 364 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.77 % Allowed : 22.13 % 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: 3.24 (0.47), residues: 339 helix: 2.38 (0.32), residues: 250 sheet: None (None), residues: 0 loop : 1.66 (0.77), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 36 HIS 0.004 0.002 HIS B 60 PHE 0.033 0.001 PHE B 93 TYR 0.003 0.000 TYR A 206 ARG 0.003 0.001 ARG A 78 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1374.97 seconds wall clock time: 25 minutes 12.05 seconds (1512.05 seconds total)