Starting phenix.real_space_refine on Thu Jun 5 07:25:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wus_32840/06_2025/7wus_32840.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wus_32840/06_2025/7wus_32840.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wus_32840/06_2025/7wus_32840.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wus_32840/06_2025/7wus_32840.map" model { file = "/net/cci-nas-00/data/ceres_data/7wus_32840/06_2025/7wus_32840.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wus_32840/06_2025/7wus_32840.cif" } resolution = 3.4 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 ------------------------------------------------------------------------------- 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= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 336 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 3446 2.51 5 N 946 2.21 5 O 1016 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 5450 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2725 Classifications: {'peptide': 341} Link IDs: {'CIS': 5, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 319} Restraints were copied for chains: B Time building chain proxies: 4.53, per 1000 atoms: 0.83 Number of scatterers: 5450 At special positions: 0 Unit cell: (105.6, 101.64, 67.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 1016 8.00 N 946 7.00 C 3446 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS A 15 " distance=2.03 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 143 " distance=2.03 Simple disulfide: pdb=" SG CYS A 179 " - pdb=" SG CYS A 223 " distance=2.03 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 329 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 312 " distance=2.03 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 316 " distance=2.03 Simple disulfide: pdb=" SG CYS B 4 " - pdb=" SG CYS B 15 " distance=2.03 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS B 143 " distance=2.03 Simple disulfide: pdb=" SG CYS B 179 " - pdb=" SG CYS B 223 " distance=2.03 Simple disulfide: pdb=" SG CYS B 280 " - pdb=" SG CYS B 329 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 312 " distance=2.03 Simple disulfide: pdb=" SG CYS B 313 " - pdb=" SG CYS B 316 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.18 Conformation dependent library (CDL) restraints added in 607.7 milliseconds 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1264 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 11 sheets defined 16.1% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 38 through 50 removed outlier: 4.242A pdb=" N LEU A 42 " --> pdb=" O SER A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 53 No H-bonds generated for 'chain 'A' and resid 51 through 53' Processing helix chain 'A' and resid 61 through 69 removed outlier: 3.653A pdb=" N LYS A 69 " --> pdb=" O ASN A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 82 Processing helix chain 'A' and resid 144 through 146 No H-bonds generated for 'chain 'A' and resid 144 through 146' Processing helix chain 'A' and resid 226 through 230 removed outlier: 3.731A pdb=" N THR A 230 " --> pdb=" O LYS A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 248 Processing helix chain 'A' and resid 252 through 256 removed outlier: 3.574A pdb=" N ASN A 255 " --> pdb=" O SER A 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 50 removed outlier: 4.242A pdb=" N LEU B 42 " --> pdb=" O SER B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 53 No H-bonds generated for 'chain 'B' and resid 51 through 53' Processing helix chain 'B' and resid 61 through 69 removed outlier: 3.652A pdb=" N LYS B 69 " --> pdb=" O ASN B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 82 Processing helix chain 'B' and resid 144 through 146 No H-bonds generated for 'chain 'B' and resid 144 through 146' Processing helix chain 'B' and resid 226 through 230 removed outlier: 3.731A pdb=" N THR B 230 " --> pdb=" O LYS B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 248 Processing helix chain 'B' and resid 252 through 256 removed outlier: 3.575A pdb=" N ASN B 255 " --> pdb=" O SER B 252 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 16 removed outlier: 3.561A pdb=" N GLU A 12 " --> pdb=" O SER A 7 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N CYS A 4 " --> pdb=" O CYS B 4 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N CYS B 4 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU B 12 " --> pdb=" O SER B 7 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 21 Processing sheet with id=AA3, first strand: chain 'A' and resid 34 through 36 removed outlier: 7.483A pdb=" N GLN A 35 " --> pdb=" O LEU A 169 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N TRP A 168 " --> pdb=" O GLU A 156 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 87 through 89 removed outlier: 6.267A pdb=" N THR A 87 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N ILE A 135 " --> pdb=" O THR A 87 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N MET A 89 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLY A 56 " --> pdb=" O ALA A 149 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 273 through 275 removed outlier: 5.213A pdb=" N ILE A 212 " --> pdb=" O ALA A 205 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ALA A 205 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER A 216 " --> pdb=" O TRP A 201 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG A 192 " --> pdb=" O LYS A 189 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA A 186 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA B 186 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG B 192 " --> pdb=" O LYS B 189 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N SER B 216 " --> pdb=" O TRP B 201 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ALA B 205 " --> pdb=" O ILE B 212 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ILE B 212 " --> pdb=" O ALA B 205 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 284 through 287 Processing sheet with id=AA7, first strand: chain 'A' and resid 322 through 324 Processing sheet with id=AA8, first strand: chain 'B' and resid 34 through 36 removed outlier: 7.484A pdb=" N GLN B 35 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N TRP B 168 " --> pdb=" O GLU B 156 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 87 through 89 removed outlier: 6.267A pdb=" N THR B 87 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N ILE B 135 " --> pdb=" O THR B 87 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N MET B 89 " --> pdb=" O ILE B 135 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N GLY B 56 " --> pdb=" O ALA B 149 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 284 through 287 Processing sheet with id=AB2, first strand: chain 'B' and resid 322 through 324 118 hydrogen bonds defined for protein. 294 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: 1.46 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1762 1.34 - 1.46: 1309 1.46 - 1.58: 2463 1.58 - 1.70: 0 1.70 - 1.81: 60 Bond restraints: 5594 Sorted by residual: bond pdb=" N GLN B 107 " pdb=" CA GLN B 107 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.83e+00 bond pdb=" N GLN A 107 " pdb=" CA GLN A 107 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.79e+00 bond pdb=" C PRO A 106 " pdb=" N GLN A 107 " ideal model delta sigma weight residual 1.329 1.349 -0.020 1.40e-02 5.10e+03 1.95e+00 bond pdb=" C PRO B 106 " pdb=" N GLN B 107 " ideal model delta sigma weight residual 1.329 1.347 -0.018 1.40e-02 5.10e+03 1.64e+00 bond pdb=" CA TYR B 32 " pdb=" C TYR B 32 " ideal model delta sigma weight residual 1.523 1.538 -0.014 1.30e-02 5.92e+03 1.22e+00 ... (remaining 5589 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 7441 2.33 - 4.65: 115 4.65 - 6.98: 12 6.98 - 9.31: 8 9.31 - 11.64: 4 Bond angle restraints: 7580 Sorted by residual: angle pdb=" C PRO B 106 " pdb=" N GLN B 107 " pdb=" CA GLN B 107 " ideal model delta sigma weight residual 121.70 133.34 -11.64 1.80e+00 3.09e-01 4.18e+01 angle pdb=" C PRO A 106 " pdb=" N GLN A 107 " pdb=" CA GLN A 107 " ideal model delta sigma weight residual 121.70 133.32 -11.62 1.80e+00 3.09e-01 4.17e+01 angle pdb=" C TYR B 32 " pdb=" N LYS B 33 " pdb=" CA LYS B 33 " ideal model delta sigma weight residual 121.70 131.65 -9.95 1.80e+00 3.09e-01 3.06e+01 angle pdb=" C TYR A 32 " pdb=" N LYS A 33 " pdb=" CA LYS A 33 " ideal model delta sigma weight residual 121.70 131.63 -9.93 1.80e+00 3.09e-01 3.04e+01 angle pdb=" C LYS B 189 " pdb=" N ASP B 190 " pdb=" CA ASP B 190 " ideal model delta sigma weight residual 121.54 128.85 -7.31 1.91e+00 2.74e-01 1.47e+01 ... (remaining 7575 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.00: 2734 16.00 - 32.00: 466 32.00 - 48.00: 124 48.00 - 64.00: 22 64.00 - 80.00: 10 Dihedral angle restraints: 3356 sinusoidal: 1396 harmonic: 1960 Sorted by residual: dihedral pdb=" CA GLN B 31 " pdb=" C GLN B 31 " pdb=" N TYR B 32 " pdb=" CA TYR B 32 " ideal model delta harmonic sigma weight residual -180.00 -154.44 -25.56 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA GLN A 31 " pdb=" C GLN A 31 " pdb=" N TYR A 32 " pdb=" CA TYR A 32 " ideal model delta harmonic sigma weight residual -180.00 -154.47 -25.53 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 312 " pdb=" CB CYS B 312 " ideal model delta sinusoidal sigma weight residual 93.00 54.60 38.40 1 1.00e+01 1.00e-02 2.08e+01 ... (remaining 3353 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 628 0.047 - 0.093: 129 0.093 - 0.140: 41 0.140 - 0.186: 6 0.186 - 0.233: 4 Chirality restraints: 808 Sorted by residual: chirality pdb=" CA GLN A 107 " pdb=" N GLN A 107 " pdb=" C GLN A 107 " pdb=" CB GLN A 107 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA GLN B 107 " pdb=" N GLN B 107 " pdb=" C GLN B 107 " pdb=" CB GLN B 107 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CB ILE A 167 " pdb=" CA ILE A 167 " pdb=" CG1 ILE A 167 " pdb=" CG2 ILE A 167 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 805 not shown) Planarity restraints: 962 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 189 " 0.007 2.00e-02 2.50e+03 1.45e-02 2.09e+00 pdb=" C LYS A 189 " -0.025 2.00e-02 2.50e+03 pdb=" O LYS A 189 " 0.010 2.00e-02 2.50e+03 pdb=" N ASP A 190 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 189 " -0.007 2.00e-02 2.50e+03 1.44e-02 2.07e+00 pdb=" C LYS B 189 " 0.025 2.00e-02 2.50e+03 pdb=" O LYS B 189 " -0.009 2.00e-02 2.50e+03 pdb=" N ASP B 190 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 277 " 0.005 2.00e-02 2.50e+03 1.08e-02 1.17e+00 pdb=" C PHE A 277 " -0.019 2.00e-02 2.50e+03 pdb=" O PHE A 277 " 0.007 2.00e-02 2.50e+03 pdb=" N ASP A 278 " 0.006 2.00e-02 2.50e+03 ... (remaining 959 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1513 2.80 - 3.33: 4826 3.33 - 3.85: 8758 3.85 - 4.38: 9812 4.38 - 4.90: 16744 Nonbonded interactions: 41653 Sorted by model distance: nonbonded pdb=" O THR B 164 " pdb=" OG1 THR B 165 " model vdw 2.275 3.040 nonbonded pdb=" O THR A 164 " pdb=" OG1 THR A 165 " model vdw 2.276 3.040 nonbonded pdb=" O ARG A 105 " pdb=" NE2 GLN A 107 " model vdw 2.287 3.120 nonbonded pdb=" O ARG B 105 " pdb=" NE2 GLN B 107 " model vdw 2.288 3.120 nonbonded pdb=" OD1 ASP A 176 " pdb=" N PHE A 178 " model vdw 2.295 3.120 ... (remaining 41648 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 16.890 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 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:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 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 : 0.003 0.032 5606 Z= 0.129 Angle : 0.747 11.636 7604 Z= 0.403 Chirality : 0.046 0.233 808 Planarity : 0.004 0.038 962 Dihedral : 17.105 79.998 2056 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 1.00 % Allowed : 24.08 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.54 % 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: -2.40 (0.32), residues: 678 helix: -0.05 (0.70), residues: 64 sheet: -1.82 (0.40), residues: 156 loop : -1.82 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 225 HIS 0.002 0.000 HIS A 195 PHE 0.009 0.001 PHE B 217 TYR 0.012 0.001 TYR B 32 ARG 0.009 0.001 ARG A 324 Details of bonding type rmsd hydrogen bonds : bond 0.21900 ( 118) hydrogen bonds : angle 11.00360 ( 294) SS BOND : bond 0.00135 ( 12) SS BOND : angle 0.34122 ( 24) covalent geometry : bond 0.00262 ( 5594) covalent geometry : angle 0.74839 ( 7580) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 127 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 34 PHE cc_start: 0.7575 (m-80) cc_final: 0.7175 (m-80) REVERT: B 35 GLN cc_start: 0.7206 (pt0) cc_final: 0.6988 (pt0) REVERT: B 62 ARG cc_start: 0.7403 (ptp-110) cc_final: 0.7115 (ttt-90) REVERT: B 232 TRP cc_start: 0.8435 (t60) cc_final: 0.8181 (t60) outliers start: 6 outliers final: 2 residues processed: 129 average time/residue: 0.2223 time to fit residues: 35.3255 Evaluate side-chains 88 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 86 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain B residue 165 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 57 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 chunk 34 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 chunk 61 optimal weight: 4.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 ASN A 31 GLN ** A 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 10 ASN ** B 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 GLN B 151 ASN ** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.174306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.130615 restraints weight = 7518.468| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 3.82 r_work: 0.3494 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 5606 Z= 0.346 Angle : 0.888 11.988 7604 Z= 0.470 Chirality : 0.051 0.222 808 Planarity : 0.006 0.038 962 Dihedral : 6.755 51.684 728 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.62 % Favored : 89.38 % Rotamer: Outliers : 6.02 % Allowed : 22.91 % Favored : 71.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.54 % 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: -2.59 (0.32), residues: 678 helix: -0.72 (0.65), residues: 68 sheet: -1.86 (0.38), residues: 170 loop : -1.89 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 311 HIS 0.011 0.002 HIS A 195 PHE 0.021 0.003 PHE A 217 TYR 0.020 0.003 TYR A 32 ARG 0.006 0.001 ARG A 257 Details of bonding type rmsd hydrogen bonds : bond 0.04414 ( 118) hydrogen bonds : angle 8.03654 ( 294) SS BOND : bond 0.00386 ( 12) SS BOND : angle 0.76753 ( 24) covalent geometry : bond 0.00791 ( 5594) covalent geometry : angle 0.88837 ( 7580) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 75 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 272 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.7605 (mmt90) REVERT: B 232 TRP cc_start: 0.9013 (t60) cc_final: 0.8705 (t60) REVERT: B 314 ARG cc_start: 0.8261 (ttm-80) cc_final: 0.7837 (mtt-85) outliers start: 36 outliers final: 16 residues processed: 100 average time/residue: 0.1810 time to fit residues: 23.9299 Evaluate side-chains 88 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 191 ASN Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 131 HIS Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 297 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 31 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 12 optimal weight: 8.9990 chunk 34 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 31 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.181147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.131363 restraints weight = 7249.968| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 3.66 r_work: 0.3571 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5606 Z= 0.139 Angle : 0.752 11.775 7604 Z= 0.397 Chirality : 0.047 0.230 808 Planarity : 0.004 0.034 962 Dihedral : 5.738 25.741 726 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 4.52 % Allowed : 22.41 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.54 % 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: -2.28 (0.32), residues: 678 helix: -0.19 (0.67), residues: 68 sheet: -1.79 (0.39), residues: 176 loop : -1.66 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 225 HIS 0.005 0.001 HIS B 195 PHE 0.010 0.001 PHE A 133 TYR 0.016 0.001 TYR B 32 ARG 0.005 0.000 ARG B 324 Details of bonding type rmsd hydrogen bonds : bond 0.03344 ( 118) hydrogen bonds : angle 7.42436 ( 294) SS BOND : bond 0.00191 ( 12) SS BOND : angle 0.65026 ( 24) covalent geometry : bond 0.00309 ( 5594) covalent geometry : angle 0.75241 ( 7580) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 84 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 GLN cc_start: 0.8386 (pp30) cc_final: 0.8028 (pp30) REVERT: A 333 MET cc_start: 0.7879 (ttm) cc_final: 0.7551 (ttm) REVERT: B 62 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7492 (ttt-90) REVERT: B 67 MET cc_start: 0.8980 (tmm) cc_final: 0.8765 (tmm) REVERT: B 232 TRP cc_start: 0.8879 (t60) cc_final: 0.8533 (t60) REVERT: B 324 ARG cc_start: 0.8185 (mtt-85) cc_final: 0.7927 (mtt90) outliers start: 27 outliers final: 13 residues processed: 100 average time/residue: 0.1702 time to fit residues: 23.0469 Evaluate side-chains 95 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 131 HIS Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 276 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 20 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 chunk 1 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.179633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.129802 restraints weight = 7412.307| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 3.64 r_work: 0.3583 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5606 Z= 0.163 Angle : 0.753 11.787 7604 Z= 0.393 Chirality : 0.048 0.232 808 Planarity : 0.004 0.034 962 Dihedral : 5.663 27.394 726 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer: Outliers : 4.18 % Allowed : 22.91 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.54 % 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: -2.16 (0.33), residues: 678 helix: 0.03 (0.67), residues: 68 sheet: -1.68 (0.39), residues: 176 loop : -1.61 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 28 HIS 0.005 0.001 HIS B 195 PHE 0.020 0.002 PHE A 133 TYR 0.017 0.002 TYR B 32 ARG 0.003 0.000 ARG B 324 Details of bonding type rmsd hydrogen bonds : bond 0.03206 ( 118) hydrogen bonds : angle 7.10035 ( 294) SS BOND : bond 0.00197 ( 12) SS BOND : angle 0.56387 ( 24) covalent geometry : bond 0.00368 ( 5594) covalent geometry : angle 0.75306 ( 7580) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 82 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 GLN cc_start: 0.8367 (pp30) cc_final: 0.8031 (pp30) REVERT: A 333 MET cc_start: 0.8016 (ttm) cc_final: 0.7662 (ttp) REVERT: B 34 PHE cc_start: 0.8387 (m-80) cc_final: 0.8041 (m-80) REVERT: B 62 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7629 (ttt-90) REVERT: B 83 GLU cc_start: 0.8116 (mp0) cc_final: 0.7718 (tm-30) REVERT: B 232 TRP cc_start: 0.8911 (t60) cc_final: 0.8599 (t60) REVERT: B 314 ARG cc_start: 0.8245 (ttm-80) cc_final: 0.7854 (mtt-85) outliers start: 25 outliers final: 18 residues processed: 96 average time/residue: 0.1832 time to fit residues: 23.3043 Evaluate side-chains 98 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 131 HIS Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain B residue 276 ASP Chi-restraints excluded: chain B residue 333 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 51 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 62 optimal weight: 0.0010 chunk 33 optimal weight: 0.5980 chunk 10 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 overall best weight: 1.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.180806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.131210 restraints weight = 7233.830| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 3.60 r_work: 0.3603 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5606 Z= 0.138 Angle : 0.722 11.755 7604 Z= 0.378 Chirality : 0.047 0.234 808 Planarity : 0.004 0.032 962 Dihedral : 5.571 27.044 726 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 4.52 % Allowed : 23.58 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.54 % 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: -2.04 (0.33), residues: 678 helix: 0.16 (0.68), residues: 68 sheet: -1.58 (0.40), residues: 176 loop : -1.54 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 225 HIS 0.004 0.001 HIS B 195 PHE 0.017 0.002 PHE A 133 TYR 0.018 0.001 TYR B 32 ARG 0.004 0.000 ARG B 322 Details of bonding type rmsd hydrogen bonds : bond 0.02955 ( 118) hydrogen bonds : angle 6.88447 ( 294) SS BOND : bond 0.00176 ( 12) SS BOND : angle 0.50627 ( 24) covalent geometry : bond 0.00310 ( 5594) covalent geometry : angle 0.72262 ( 7580) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 84 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.5136 (OUTLIER) cc_final: 0.4915 (tt0) REVERT: A 175 GLN cc_start: 0.8292 (pp30) cc_final: 0.8028 (pp30) REVERT: A 272 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.7473 (mmt90) REVERT: A 333 MET cc_start: 0.7901 (ttm) cc_final: 0.7618 (ttm) REVERT: B 34 PHE cc_start: 0.8336 (m-80) cc_final: 0.7588 (m-80) REVERT: B 62 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7627 (ttt-90) REVERT: B 123 MET cc_start: 0.1961 (ttp) cc_final: 0.1669 (tmm) REVERT: B 180 ASP cc_start: 0.7262 (OUTLIER) cc_final: 0.7008 (m-30) REVERT: B 232 TRP cc_start: 0.8889 (t60) cc_final: 0.8595 (t60) outliers start: 27 outliers final: 19 residues processed: 99 average time/residue: 0.1691 time to fit residues: 22.1683 Evaluate side-chains 101 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 78 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain B residue 329 CYS Chi-restraints excluded: chain B residue 333 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 63 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 44 optimal weight: 0.2980 chunk 51 optimal weight: 1.9990 chunk 41 optimal weight: 0.0370 chunk 19 optimal weight: 5.9990 chunk 25 optimal weight: 0.0670 chunk 23 optimal weight: 0.0670 chunk 36 optimal weight: 8.9990 chunk 59 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 overall best weight: 0.4936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.194422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.140525 restraints weight = 7409.104| |-----------------------------------------------------------------------------| r_work (start): 0.3898 rms_B_bonded: 3.92 r_work: 0.3733 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5606 Z= 0.115 Angle : 0.695 11.746 7604 Z= 0.363 Chirality : 0.046 0.233 808 Planarity : 0.004 0.031 962 Dihedral : 5.242 25.890 726 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 3.68 % Allowed : 23.75 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.54 % 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: -1.92 (0.33), residues: 678 helix: 0.23 (0.67), residues: 68 sheet: -1.24 (0.41), residues: 154 loop : -1.60 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 225 HIS 0.003 0.000 HIS B 195 PHE 0.012 0.001 PHE A 133 TYR 0.018 0.001 TYR B 32 ARG 0.002 0.000 ARG B 324 Details of bonding type rmsd hydrogen bonds : bond 0.02790 ( 118) hydrogen bonds : angle 6.57918 ( 294) SS BOND : bond 0.00111 ( 12) SS BOND : angle 0.43460 ( 24) covalent geometry : bond 0.00246 ( 5594) covalent geometry : angle 0.69578 ( 7580) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 87 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 GLN cc_start: 0.8346 (pp30) cc_final: 0.7999 (pp30) REVERT: A 278 ASP cc_start: 0.8056 (m-30) cc_final: 0.7810 (m-30) REVERT: B 62 ARG cc_start: 0.8112 (ptp-110) cc_final: 0.7510 (ttt-90) REVERT: B 180 ASP cc_start: 0.7234 (OUTLIER) cc_final: 0.6995 (m-30) REVERT: B 232 TRP cc_start: 0.8815 (t60) cc_final: 0.8459 (t60) outliers start: 22 outliers final: 14 residues processed: 101 average time/residue: 0.1569 time to fit residues: 21.2888 Evaluate side-chains 95 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 329 CYS Chi-restraints excluded: chain B residue 333 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 25 optimal weight: 0.0980 chunk 53 optimal weight: 0.0870 chunk 45 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 64 optimal weight: 0.0170 chunk 20 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 30 optimal weight: 10.0000 chunk 27 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 overall best weight: 0.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.187545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.137224 restraints weight = 7195.959| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 3.73 r_work: 0.3771 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5606 Z= 0.115 Angle : 0.715 11.700 7604 Z= 0.371 Chirality : 0.046 0.232 808 Planarity : 0.003 0.030 962 Dihedral : 5.078 25.293 726 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 4.18 % Allowed : 22.91 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.54 % 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: -1.79 (0.33), residues: 678 helix: 0.23 (0.66), residues: 68 sheet: -0.86 (0.44), residues: 142 loop : -1.60 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 225 HIS 0.002 0.000 HIS B 195 PHE 0.010 0.001 PHE A 133 TYR 0.020 0.001 TYR B 32 ARG 0.004 0.000 ARG B 324 Details of bonding type rmsd hydrogen bonds : bond 0.02637 ( 118) hydrogen bonds : angle 6.41461 ( 294) SS BOND : bond 0.00105 ( 12) SS BOND : angle 0.38378 ( 24) covalent geometry : bond 0.00245 ( 5594) covalent geometry : angle 0.71552 ( 7580) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 88 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 GLN cc_start: 0.8296 (pp30) cc_final: 0.7903 (pp30) REVERT: A 278 ASP cc_start: 0.8071 (m-30) cc_final: 0.7778 (m-30) REVERT: A 331 TYR cc_start: 0.8656 (m-80) cc_final: 0.7955 (t80) REVERT: B 32 TYR cc_start: 0.6224 (OUTLIER) cc_final: 0.5181 (p90) REVERT: B 62 ARG cc_start: 0.7833 (ptp-110) cc_final: 0.7150 (ttt-90) REVERT: B 180 ASP cc_start: 0.7147 (OUTLIER) cc_final: 0.6897 (m-30) REVERT: B 232 TRP cc_start: 0.8741 (t60) cc_final: 0.8321 (t60) outliers start: 25 outliers final: 16 residues processed: 104 average time/residue: 0.1419 time to fit residues: 20.4738 Evaluate side-chains 96 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 32 TYR Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 329 CYS Chi-restraints excluded: chain B residue 333 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 56 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 24 optimal weight: 0.2980 chunk 66 optimal weight: 4.9990 chunk 23 optimal weight: 0.0870 chunk 39 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 8 optimal weight: 9.9990 chunk 41 optimal weight: 0.9990 overall best weight: 1.2764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 129 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.182027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.131771 restraints weight = 7197.186| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 3.73 r_work: 0.3699 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5606 Z= 0.156 Angle : 0.727 11.685 7604 Z= 0.382 Chirality : 0.046 0.233 808 Planarity : 0.004 0.032 962 Dihedral : 5.244 26.499 726 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 3.34 % Allowed : 24.75 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.54 % 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: -1.90 (0.33), residues: 678 helix: 0.13 (0.67), residues: 68 sheet: -1.05 (0.43), residues: 150 loop : -1.64 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 28 HIS 0.005 0.001 HIS B 195 PHE 0.017 0.002 PHE B 34 TYR 0.021 0.002 TYR B 32 ARG 0.005 0.000 ARG B 324 Details of bonding type rmsd hydrogen bonds : bond 0.02882 ( 118) hydrogen bonds : angle 6.49121 ( 294) SS BOND : bond 0.00174 ( 12) SS BOND : angle 0.50648 ( 24) covalent geometry : bond 0.00353 ( 5594) covalent geometry : angle 0.72758 ( 7580) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 76 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 GLN cc_start: 0.8257 (pp30) cc_final: 0.7874 (pp30) REVERT: A 184 MET cc_start: 0.8577 (mtp) cc_final: 0.8244 (mtp) REVERT: A 272 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.7561 (mmt90) REVERT: B 32 TYR cc_start: 0.6335 (OUTLIER) cc_final: 0.5377 (p90) REVERT: B 232 TRP cc_start: 0.8864 (t60) cc_final: 0.8518 (t60) outliers start: 20 outliers final: 15 residues processed: 89 average time/residue: 0.1572 time to fit residues: 18.6757 Evaluate side-chains 89 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain B residue 32 TYR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 329 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 10 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 29 optimal weight: 0.0470 chunk 0 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 overall best weight: 1.1884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.181727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.131855 restraints weight = 7288.180| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 3.74 r_work: 0.3696 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5606 Z= 0.150 Angle : 0.731 11.682 7604 Z= 0.381 Chirality : 0.047 0.234 808 Planarity : 0.004 0.035 962 Dihedral : 5.279 26.957 726 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 3.34 % Allowed : 24.75 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.54 % 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: -1.83 (0.33), residues: 678 helix: 0.30 (0.68), residues: 66 sheet: -1.03 (0.44), residues: 150 loop : -1.59 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 225 HIS 0.006 0.001 HIS B 195 PHE 0.011 0.002 PHE B 34 TYR 0.019 0.002 TYR B 32 ARG 0.004 0.000 ARG B 324 Details of bonding type rmsd hydrogen bonds : bond 0.02865 ( 118) hydrogen bonds : angle 6.46315 ( 294) SS BOND : bond 0.00163 ( 12) SS BOND : angle 0.50236 ( 24) covalent geometry : bond 0.00340 ( 5594) covalent geometry : angle 0.73204 ( 7580) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 GLN cc_start: 0.8310 (pp30) cc_final: 0.7908 (pp30) REVERT: A 184 MET cc_start: 0.8513 (mtp) cc_final: 0.8140 (mtp) REVERT: A 272 ARG cc_start: 0.7970 (OUTLIER) cc_final: 0.7542 (mmt90) REVERT: A 278 ASP cc_start: 0.8019 (m-30) cc_final: 0.7701 (m-30) REVERT: B 32 TYR cc_start: 0.6205 (OUTLIER) cc_final: 0.5588 (p90) REVERT: B 232 TRP cc_start: 0.8848 (t60) cc_final: 0.8499 (t60) outliers start: 20 outliers final: 17 residues processed: 95 average time/residue: 0.1417 time to fit residues: 18.5519 Evaluate side-chains 97 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain B residue 32 TYR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 329 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 41 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 58 optimal weight: 0.0020 chunk 52 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 36 optimal weight: 0.0970 chunk 49 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 overall best weight: 0.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.182957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.133056 restraints weight = 7290.907| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 3.74 r_work: 0.3710 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5606 Z= 0.136 Angle : 0.724 11.705 7604 Z= 0.378 Chirality : 0.047 0.232 808 Planarity : 0.004 0.035 962 Dihedral : 5.230 26.636 726 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 3.01 % Allowed : 25.25 % Favored : 71.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.54 % 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: -1.76 (0.33), residues: 678 helix: 0.29 (0.68), residues: 66 sheet: -0.82 (0.44), residues: 142 loop : -1.59 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 225 HIS 0.005 0.001 HIS B 195 PHE 0.015 0.002 PHE B 34 TYR 0.020 0.001 TYR B 32 ARG 0.005 0.000 ARG B 324 Details of bonding type rmsd hydrogen bonds : bond 0.02771 ( 118) hydrogen bonds : angle 6.36182 ( 294) SS BOND : bond 0.00147 ( 12) SS BOND : angle 0.48710 ( 24) covalent geometry : bond 0.00305 ( 5594) covalent geometry : angle 0.72480 ( 7580) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 GLN cc_start: 0.8362 (pp30) cc_final: 0.7942 (pp30) REVERT: A 184 MET cc_start: 0.8519 (mtp) cc_final: 0.8215 (mtp) REVERT: A 272 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7500 (mmt90) REVERT: A 278 ASP cc_start: 0.8038 (m-30) cc_final: 0.7664 (m-30) REVERT: B 32 TYR cc_start: 0.6109 (OUTLIER) cc_final: 0.5346 (p90) REVERT: B 232 TRP cc_start: 0.8865 (t60) cc_final: 0.8525 (t60) outliers start: 18 outliers final: 14 residues processed: 87 average time/residue: 0.1886 time to fit residues: 22.7845 Evaluate side-chains 94 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain B residue 32 TYR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 329 CYS Chi-restraints excluded: chain B residue 333 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 56 optimal weight: 0.6980 chunk 2 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 66 optimal weight: 0.8980 chunk 16 optimal weight: 0.0020 chunk 25 optimal weight: 0.0050 chunk 23 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 overall best weight: 0.4402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.188626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.138905 restraints weight = 7281.488| |-----------------------------------------------------------------------------| r_work (start): 0.3921 rms_B_bonded: 3.81 r_work: 0.3760 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5606 Z= 0.116 Angle : 0.705 11.720 7604 Z= 0.367 Chirality : 0.046 0.230 808 Planarity : 0.004 0.033 962 Dihedral : 5.026 25.799 726 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 3.01 % Allowed : 25.08 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.54 % 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: -1.66 (0.33), residues: 678 helix: 0.41 (0.68), residues: 66 sheet: -0.74 (0.44), residues: 142 loop : -1.53 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 225 HIS 0.002 0.000 HIS B 195 PHE 0.013 0.001 PHE B 34 TYR 0.019 0.001 TYR B 32 ARG 0.005 0.000 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.02600 ( 118) hydrogen bonds : angle 6.10441 ( 294) SS BOND : bond 0.00105 ( 12) SS BOND : angle 0.40595 ( 24) covalent geometry : bond 0.00252 ( 5594) covalent geometry : angle 0.70548 ( 7580) =============================================================================== Job complete usr+sys time: 3378.44 seconds wall clock time: 60 minutes 24.12 seconds (3624.12 seconds total)