Starting phenix.real_space_refine on Sun Jul 27 09:30:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ajq_11806/07_2025/7ajq_11806.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ajq_11806/07_2025/7ajq_11806.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ajq_11806/07_2025/7ajq_11806.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ajq_11806/07_2025/7ajq_11806.map" model { file = "/net/cci-nas-00/data/ceres_data/7ajq_11806/07_2025/7ajq_11806.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ajq_11806/07_2025/7ajq_11806.cif" } resolution = 4.0 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= 0.074 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: 4 Type Number sf(0) Gaussians S 29 5.16 5 C 5817 2.51 5 N 1675 2.21 5 O 1689 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 9210 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1729 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 225} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1777 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 231} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1777 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 231} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1777 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 231} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1777 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 231} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 177 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 2, 'TRANS': 20} Chain: "G" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 196 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 2, 'TRANS': 22} Time building chain proxies: 6.29, per 1000 atoms: 0.68 Number of scatterers: 9210 At special positions: 0 Unit cell: (84.293, 87.494, 133.375, 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 29 16.00 O 1689 8.00 N 1675 7.00 C 5817 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: 2.70 Conformation dependent library (CDL) restraints added in 1.2 seconds 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2246 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 0 sheets defined 87.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 57 through 100 Processing helix chain 'A' and resid 104 through 113 removed outlier: 3.530A pdb=" N ALA A 108 " --> pdb=" O SER A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 136 Processing helix chain 'A' and resid 140 through 164 Processing helix chain 'A' and resid 166 through 199 Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 206 through 272 removed outlier: 4.633A pdb=" N GLY A 210 " --> pdb=" O VAL A 206 " (cutoff:3.500A) Proline residue: A 227 - end of helix removed outlier: 4.246A pdb=" N ALA A 267 " --> pdb=" O LEU A 263 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU A 268 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER A 272 " --> pdb=" O GLU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 280 removed outlier: 3.509A pdb=" N HIS A 276 " --> pdb=" O SER A 272 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN A 277 " --> pdb=" O GLN A 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 100 Processing helix chain 'B' and resid 104 through 114 removed outlier: 4.395A pdb=" N ASN B 114 " --> pdb=" O GLU B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 136 Processing helix chain 'B' and resid 140 through 164 Processing helix chain 'B' and resid 165 through 199 removed outlier: 4.107A pdb=" N PHE B 169 " --> pdb=" O ARG B 165 " (cutoff:3.500A) Proline residue: B 178 - end of helix Processing helix chain 'B' and resid 206 through 280 removed outlier: 4.098A pdb=" N GLY B 210 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE B 211 " --> pdb=" O VAL B 207 " (cutoff:3.500A) Proline residue: B 227 - end of helix removed outlier: 4.524A pdb=" N ALA B 267 " --> pdb=" O LEU B 263 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N GLU B 268 " --> pdb=" O ALA B 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 53 removed outlier: 4.207A pdb=" N TYR C 53 " --> pdb=" O ILE C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 100 Processing helix chain 'C' and resid 105 through 113 Processing helix chain 'C' and resid 119 through 135 Processing helix chain 'C' and resid 140 through 164 removed outlier: 3.608A pdb=" N ILE C 144 " --> pdb=" O ASP C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 199 Proline residue: C 178 - end of helix Processing helix chain 'C' and resid 207 through 280 Proline residue: C 227 - end of helix removed outlier: 4.447A pdb=" N ALA C 267 " --> pdb=" O LEU C 263 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLU C 268 " --> pdb=" O ALA C 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 52 Processing helix chain 'D' and resid 57 through 99 Processing helix chain 'D' and resid 100 through 102 No H-bonds generated for 'chain 'D' and resid 100 through 102' Processing helix chain 'D' and resid 104 through 114 removed outlier: 3.515A pdb=" N ASN D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 135 Processing helix chain 'D' and resid 140 through 164 Processing helix chain 'D' and resid 165 through 199 removed outlier: 4.232A pdb=" N PHE D 169 " --> pdb=" O ARG D 165 " (cutoff:3.500A) Proline residue: D 178 - end of helix Processing helix chain 'D' and resid 204 through 206 No H-bonds generated for 'chain 'D' and resid 204 through 206' Processing helix chain 'D' and resid 207 through 272 removed outlier: 3.506A pdb=" N ILE D 211 " --> pdb=" O VAL D 207 " (cutoff:3.500A) Proline residue: D 227 - end of helix removed outlier: 3.908A pdb=" N ALA D 267 " --> pdb=" O LEU D 263 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU D 268 " --> pdb=" O ALA D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 277 removed outlier: 4.551A pdb=" N GLN D 277 " --> pdb=" O GLN D 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 100 Processing helix chain 'E' and resid 104 through 113 Processing helix chain 'E' and resid 119 through 135 Processing helix chain 'E' and resid 140 through 164 Processing helix chain 'E' and resid 166 through 199 Proline residue: E 178 - end of helix Processing helix chain 'E' and resid 207 through 277 removed outlier: 3.945A pdb=" N ILE E 211 " --> pdb=" O VAL E 207 " (cutoff:3.500A) Proline residue: E 227 - end of helix Processing helix chain 'F' and resid 22 through 38 removed outlier: 4.068A pdb=" N VAL F 26 " --> pdb=" O PRO F 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 38 removed outlier: 4.168A pdb=" N ASP G 25 " --> pdb=" O THR G 21 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL G 26 " --> pdb=" O PRO G 22 " (cutoff:3.500A) 865 hydrogen bonds defined for protein. 2589 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: 2.56 Time building geometry restraints manager: 3.14 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: 3175 1.34 - 1.46: 1464 1.46 - 1.57: 4643 1.57 - 1.69: 0 1.69 - 1.81: 58 Bond restraints: 9340 Sorted by residual: bond pdb=" C THR F 21 " pdb=" N PRO F 22 " ideal model delta sigma weight residual 1.337 1.369 -0.033 9.80e-03 1.04e+04 1.11e+01 bond pdb=" C HIS E 276 " pdb=" O HIS E 276 " ideal model delta sigma weight residual 1.235 1.249 -0.014 1.43e-02 4.89e+03 1.00e+00 bond pdb=" CA ALA A 136 " pdb=" C ALA A 136 " ideal model delta sigma weight residual 1.532 1.523 0.009 9.60e-03 1.09e+04 9.64e-01 bond pdb=" CA THR F 21 " pdb=" C THR F 21 " ideal model delta sigma weight residual 1.524 1.534 -0.010 1.26e-02 6.30e+03 6.14e-01 bond pdb=" C ALA F 38 " pdb=" N PRO F 39 " ideal model delta sigma weight residual 1.334 1.351 -0.017 2.34e-02 1.83e+03 5.33e-01 ... (remaining 9335 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 12474 1.64 - 3.28: 128 3.28 - 4.92: 31 4.92 - 6.56: 22 6.56 - 8.20: 2 Bond angle restraints: 12657 Sorted by residual: angle pdb=" N THR G 21 " pdb=" CA THR G 21 " pdb=" C THR G 21 " ideal model delta sigma weight residual 109.81 116.15 -6.34 2.21e+00 2.05e-01 8.23e+00 angle pdb=" N THR F 21 " pdb=" CA THR F 21 " pdb=" C THR F 21 " ideal model delta sigma weight residual 109.81 116.10 -6.29 2.21e+00 2.05e-01 8.10e+00 angle pdb=" CA LEU B 278 " pdb=" CB LEU B 278 " pdb=" CG LEU B 278 " ideal model delta sigma weight residual 116.30 108.10 8.20 3.50e+00 8.16e-02 5.49e+00 angle pdb=" N SER A 135 " pdb=" CA SER A 135 " pdb=" C SER A 135 " ideal model delta sigma weight residual 111.11 108.33 2.78 1.20e+00 6.94e-01 5.37e+00 angle pdb=" C ALA D 136 " pdb=" N GLU D 137 " pdb=" CA GLU D 137 " ideal model delta sigma weight residual 121.54 125.90 -4.36 1.91e+00 2.74e-01 5.20e+00 ... (remaining 12652 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 5113 17.43 - 34.86: 395 34.86 - 52.29: 69 52.29 - 69.72: 9 69.72 - 87.14: 8 Dihedral angle restraints: 5594 sinusoidal: 2118 harmonic: 3476 Sorted by residual: dihedral pdb=" CA LEU B 278 " pdb=" C LEU B 278 " pdb=" N ARG B 279 " pdb=" CA ARG B 279 " ideal model delta harmonic sigma weight residual 180.00 156.98 23.02 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA HIS E 276 " pdb=" C HIS E 276 " pdb=" N GLN E 277 " pdb=" CA GLN E 277 " ideal model delta harmonic sigma weight residual -180.00 -157.27 -22.73 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA THR G 21 " pdb=" C THR G 21 " pdb=" N PRO G 22 " pdb=" CA PRO G 22 " ideal model delta harmonic sigma weight residual -180.00 -158.70 -21.30 0 5.00e+00 4.00e-02 1.82e+01 ... (remaining 5591 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 935 0.025 - 0.051: 339 0.051 - 0.076: 164 0.076 - 0.102: 46 0.102 - 0.127: 18 Chirality restraints: 1502 Sorted by residual: chirality pdb=" CA THR F 21 " pdb=" N THR F 21 " pdb=" C THR F 21 " pdb=" CB THR F 21 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.13 2.00e-01 2.50e+01 4.03e-01 chirality pdb=" CB VAL A 223 " pdb=" CA VAL A 223 " pdb=" CG1 VAL A 223 " pdb=" CG2 VAL A 223 " both_signs ideal model delta sigma weight residual False -2.63 -2.51 -0.12 2.00e-01 2.50e+01 3.79e-01 chirality pdb=" CB VAL G 29 " pdb=" CA VAL G 29 " pdb=" CG1 VAL G 29 " pdb=" CG2 VAL G 29 " both_signs ideal model delta sigma weight residual False -2.63 -2.51 -0.12 2.00e-01 2.50e+01 3.73e-01 ... (remaining 1499 not shown) Planarity restraints: 1642 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS C 274 " 0.008 2.00e-02 2.50e+03 1.66e-02 2.75e+00 pdb=" C HIS C 274 " -0.029 2.00e-02 2.50e+03 pdb=" O HIS C 274 " 0.011 2.00e-02 2.50e+03 pdb=" N ALA C 275 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE G 33 " 0.006 2.00e-02 2.50e+03 1.18e-02 1.38e+00 pdb=" C ILE G 33 " -0.020 2.00e-02 2.50e+03 pdb=" O ILE G 33 " 0.008 2.00e-02 2.50e+03 pdb=" N PHE G 34 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP C 248 " -0.006 2.00e-02 2.50e+03 1.15e-02 1.32e+00 pdb=" CG ASP C 248 " 0.020 2.00e-02 2.50e+03 pdb=" OD1 ASP C 248 " -0.007 2.00e-02 2.50e+03 pdb=" OD2 ASP C 248 " -0.007 2.00e-02 2.50e+03 ... (remaining 1639 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1227 2.75 - 3.28: 10405 3.28 - 3.82: 16218 3.82 - 4.36: 17160 4.36 - 4.90: 28997 Nonbonded interactions: 74007 Sorted by model distance: nonbonded pdb=" OG1 THR E 185 " pdb=" OG1 THR E 218 " model vdw 2.208 3.040 nonbonded pdb=" O GLU D 268 " pdb=" OG SER D 272 " model vdw 2.226 3.040 nonbonded pdb=" OG SER B 104 " pdb=" OD1 ASP B 106 " model vdw 2.239 3.040 nonbonded pdb=" O ASP C 262 " pdb=" OG1 THR C 266 " model vdw 2.253 3.040 nonbonded pdb=" O ASN D 162 " pdb=" NH1 ARG D 165 " model vdw 2.263 3.120 ... (remaining 74002 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' selection = (chain 'B' and resid 52 through 281) selection = (chain 'C' and resid 52 through 281) selection = (chain 'D' and resid 52 through 281) selection = (chain 'E' and resid 52 through 281) } ncs_group { reference = chain 'F' selection = (chain 'G' and resid 18 through 40) } 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: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.810 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.040 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 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 : 0.002 0.033 9340 Z= 0.126 Angle : 0.553 8.204 12657 Z= 0.315 Chirality : 0.035 0.127 1502 Planarity : 0.003 0.029 1642 Dihedral : 13.098 87.144 3348 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.98 (0.22), residues: 1208 helix: -0.03 (0.15), residues: 1015 sheet: None (None), residues: 0 loop : -3.52 (0.36), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 187 HIS 0.003 0.001 HIS C 274 PHE 0.006 0.001 PHE C 193 TYR 0.007 0.001 TYR A 232 ARG 0.002 0.000 ARG E 271 Details of bonding type rmsd hydrogen bonds : bond 0.06438 ( 865) hydrogen bonds : angle 4.23437 ( 2589) covalent geometry : bond 0.00218 ( 9340) covalent geometry : angle 0.55305 (12657) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 304 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 PHE cc_start: 0.8721 (m-10) cc_final: 0.8438 (m-10) REVERT: A 81 LYS cc_start: 0.8074 (mmmm) cc_final: 0.7861 (mmmm) REVERT: A 126 ASN cc_start: 0.8808 (t0) cc_final: 0.8240 (p0) REVERT: A 193 PHE cc_start: 0.8916 (m-10) cc_final: 0.8473 (m-10) REVERT: A 252 GLN cc_start: 0.8769 (tt0) cc_final: 0.8555 (tm-30) REVERT: B 61 LYS cc_start: 0.3876 (tttt) cc_final: 0.2932 (mmmt) REVERT: B 81 LYS cc_start: 0.9321 (tppt) cc_final: 0.8717 (mmmt) REVERT: B 187 TRP cc_start: 0.8553 (t60) cc_final: 0.8306 (t-100) REVERT: B 270 LYS cc_start: 0.7512 (pttt) cc_final: 0.7073 (tptp) REVERT: C 169 PHE cc_start: 0.8946 (t80) cc_final: 0.8730 (t80) REVERT: C 232 TYR cc_start: 0.7957 (t80) cc_final: 0.7752 (t80) REVERT: C 245 GLN cc_start: 0.8276 (mm-40) cc_final: 0.8013 (mm-40) REVERT: C 248 ASP cc_start: 0.8370 (m-30) cc_final: 0.7993 (t70) REVERT: C 252 GLN cc_start: 0.8417 (mt0) cc_final: 0.7883 (mt0) REVERT: D 169 PHE cc_start: 0.9004 (t80) cc_final: 0.8730 (t80) REVERT: D 190 MET cc_start: 0.9085 (ppp) cc_final: 0.8739 (tmm) REVERT: D 216 LEU cc_start: 0.8898 (pp) cc_final: 0.8664 (pp) REVERT: D 220 MET cc_start: 0.9033 (mmt) cc_final: 0.8724 (mpp) REVERT: E 231 ILE cc_start: 0.9236 (mm) cc_final: 0.8990 (tp) REVERT: F 27 MET cc_start: 0.7647 (mmt) cc_final: 0.7387 (mmp) REVERT: F 34 PHE cc_start: 0.3922 (m-10) cc_final: 0.3163 (m-80) outliers start: 0 outliers final: 0 residues processed: 304 average time/residue: 0.2247 time to fit residues: 91.6604 Evaluate side-chains 224 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 0.0670 chunk 90 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 30 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 93 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 69 optimal weight: 0.0670 chunk 108 optimal weight: 7.9990 overall best weight: 0.7858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN A 245 GLN C 96 GLN C 129 GLN ** C 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 HIS ** D 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 96 GLN E 273 GLN ** E 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 19 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.078997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.064866 restraints weight = 46244.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.066207 restraints weight = 33512.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.067029 restraints weight = 26116.902| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9340 Z= 0.142 Angle : 0.698 11.276 12657 Z= 0.352 Chirality : 0.042 0.209 1502 Planarity : 0.004 0.035 1642 Dihedral : 4.073 22.731 1320 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.82 % Allowed : 14.88 % Favored : 83.30 % 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: 0.56 (0.24), residues: 1208 helix: 1.04 (0.16), residues: 1021 sheet: None (None), residues: 0 loop : -3.26 (0.39), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 75 HIS 0.012 0.001 HIS C 242 PHE 0.027 0.002 PHE B 179 TYR 0.015 0.002 TYR A 232 ARG 0.004 0.000 ARG A 155 Details of bonding type rmsd hydrogen bonds : bond 0.03618 ( 865) hydrogen bonds : angle 4.18831 ( 2589) covalent geometry : bond 0.00293 ( 9340) covalent geometry : angle 0.69832 (12657) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 256 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 ASN cc_start: 0.8854 (t0) cc_final: 0.8287 (p0) REVERT: A 140 ASP cc_start: 0.6535 (m-30) cc_final: 0.6204 (m-30) REVERT: A 142 ASN cc_start: 0.8893 (OUTLIER) cc_final: 0.8642 (m110) REVERT: A 193 PHE cc_start: 0.8838 (m-10) cc_final: 0.8520 (m-10) REVERT: A 235 PHE cc_start: 0.9119 (m-80) cc_final: 0.8734 (m-80) REVERT: A 270 LYS cc_start: 0.6493 (ptpt) cc_final: 0.5928 (tmtt) REVERT: B 52 MET cc_start: 0.6864 (ttm) cc_final: 0.6653 (ttm) REVERT: B 61 LYS cc_start: 0.3620 (tttt) cc_final: 0.2970 (mmmt) REVERT: B 81 LYS cc_start: 0.9187 (tppt) cc_final: 0.8801 (mmmt) REVERT: B 130 ASN cc_start: 0.9193 (p0) cc_final: 0.8982 (p0) REVERT: B 179 PHE cc_start: 0.8700 (m-80) cc_final: 0.8490 (m-80) REVERT: B 266 THR cc_start: 0.7329 (p) cc_final: 0.7091 (t) REVERT: B 270 LYS cc_start: 0.7581 (pttt) cc_final: 0.7149 (tptp) REVERT: C 113 GLN cc_start: 0.8012 (tm-30) cc_final: 0.7721 (tm-30) REVERT: C 169 PHE cc_start: 0.8900 (t80) cc_final: 0.8657 (t80) REVERT: C 220 MET cc_start: 0.8619 (ptt) cc_final: 0.8402 (ptt) REVERT: C 235 PHE cc_start: 0.8501 (t80) cc_final: 0.8182 (m-80) REVERT: C 245 GLN cc_start: 0.8450 (mm-40) cc_final: 0.8159 (mm-40) REVERT: C 248 ASP cc_start: 0.8580 (m-30) cc_final: 0.8141 (t70) REVERT: C 252 GLN cc_start: 0.8664 (mt0) cc_final: 0.8071 (mt0) REVERT: D 67 LEU cc_start: 0.9373 (mt) cc_final: 0.9108 (pp) REVERT: D 169 PHE cc_start: 0.8896 (t80) cc_final: 0.8549 (t80) REVERT: D 189 ILE cc_start: 0.9413 (tp) cc_final: 0.9130 (pt) REVERT: E 64 MET cc_start: 0.7937 (OUTLIER) cc_final: 0.7653 (ppp) REVERT: E 187 TRP cc_start: 0.8300 (t-100) cc_final: 0.7897 (t60) REVERT: E 270 LYS cc_start: 0.7353 (tmmt) cc_final: 0.6874 (pttt) REVERT: F 35 MET cc_start: 0.2800 (tpt) cc_final: 0.2577 (tpt) outliers start: 17 outliers final: 8 residues processed: 262 average time/residue: 0.2029 time to fit residues: 73.6659 Evaluate side-chains 234 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 224 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 245 GLN Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain F residue 24 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 12 optimal weight: 4.9990 chunk 84 optimal weight: 8.9990 chunk 95 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 116 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 6 optimal weight: 9.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 ASN B 257 GLN C 191 ASN ** C 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 GLN ** E 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.077885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.063726 restraints weight = 46610.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.064812 restraints weight = 35002.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.065584 restraints weight = 27763.823| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9340 Z= 0.151 Angle : 0.707 12.606 12657 Z= 0.354 Chirality : 0.042 0.184 1502 Planarity : 0.004 0.026 1642 Dihedral : 4.162 22.896 1320 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.57 % Allowed : 19.91 % Favored : 77.52 % 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: 0.89 (0.24), residues: 1208 helix: 1.24 (0.16), residues: 1027 sheet: None (None), residues: 0 loop : -3.12 (0.41), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 75 HIS 0.009 0.001 HIS C 242 PHE 0.039 0.002 PHE B 79 TYR 0.018 0.002 TYR B 53 ARG 0.004 0.000 ARG B 90 Details of bonding type rmsd hydrogen bonds : bond 0.03685 ( 865) hydrogen bonds : angle 4.25726 ( 2589) covalent geometry : bond 0.00308 ( 9340) covalent geometry : angle 0.70668 (12657) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 237 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 ASN cc_start: 0.8833 (t0) cc_final: 0.8257 (p0) REVERT: A 140 ASP cc_start: 0.6520 (m-30) cc_final: 0.6197 (m-30) REVERT: A 193 PHE cc_start: 0.8909 (m-10) cc_final: 0.8464 (m-10) REVERT: A 220 MET cc_start: 0.8462 (tpt) cc_final: 0.8247 (tpt) REVERT: A 235 PHE cc_start: 0.9168 (m-80) cc_final: 0.8511 (m-80) REVERT: A 270 LYS cc_start: 0.6619 (ptpt) cc_final: 0.6012 (tmtt) REVERT: B 61 LYS cc_start: 0.3526 (tttt) cc_final: 0.2942 (mmmt) REVERT: B 81 LYS cc_start: 0.9252 (tppt) cc_final: 0.8953 (mttt) REVERT: B 163 MET cc_start: 0.8621 (mmm) cc_final: 0.8164 (mmm) REVERT: B 270 LYS cc_start: 0.7487 (pttt) cc_final: 0.7052 (tptp) REVERT: C 169 PHE cc_start: 0.8920 (t80) cc_final: 0.8686 (t80) REVERT: C 235 PHE cc_start: 0.8607 (t80) cc_final: 0.8265 (m-80) REVERT: C 245 GLN cc_start: 0.8418 (mm-40) cc_final: 0.8160 (mm-40) REVERT: C 248 ASP cc_start: 0.8508 (m-30) cc_final: 0.8228 (t70) REVERT: C 252 GLN cc_start: 0.8590 (mt0) cc_final: 0.8040 (mt0) REVERT: C 277 GLN cc_start: 0.5469 (OUTLIER) cc_final: 0.5228 (pm20) REVERT: D 169 PHE cc_start: 0.8836 (t80) cc_final: 0.8477 (t80) REVERT: E 64 MET cc_start: 0.7745 (OUTLIER) cc_final: 0.7521 (ppp) REVERT: E 237 ARG cc_start: 0.8485 (mmt180) cc_final: 0.8096 (mmt180) REVERT: E 270 LYS cc_start: 0.7475 (tmmt) cc_final: 0.7061 (pttt) outliers start: 24 outliers final: 14 residues processed: 251 average time/residue: 0.2076 time to fit residues: 72.6468 Evaluate side-chains 227 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 211 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 150 PHE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 245 GLN Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 185 THR Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain G residue 21 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 57 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 70 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 chunk 80 optimal weight: 6.9990 chunk 78 optimal weight: 10.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 GLN ** C 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 GLN E 191 ASN ** E 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.077359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.063576 restraints weight = 48120.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.064825 restraints weight = 35184.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.065750 restraints weight = 27514.110| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9340 Z= 0.178 Angle : 0.732 10.471 12657 Z= 0.370 Chirality : 0.043 0.237 1502 Planarity : 0.004 0.028 1642 Dihedral : 4.313 23.969 1320 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 18.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.78 % Allowed : 22.27 % Favored : 74.95 % 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: 0.93 (0.24), residues: 1208 helix: 1.26 (0.16), residues: 1027 sheet: None (None), residues: 0 loop : -3.04 (0.41), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 75 HIS 0.006 0.001 HIS C 242 PHE 0.037 0.002 PHE B 79 TYR 0.024 0.002 TYR C 232 ARG 0.004 0.000 ARG C 237 Details of bonding type rmsd hydrogen bonds : bond 0.03777 ( 865) hydrogen bonds : angle 4.39676 ( 2589) covalent geometry : bond 0.00364 ( 9340) covalent geometry : angle 0.73180 (12657) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 226 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.9307 (pttp) cc_final: 0.8985 (tppt) REVERT: A 126 ASN cc_start: 0.8904 (t0) cc_final: 0.8317 (p0) REVERT: A 140 ASP cc_start: 0.6858 (m-30) cc_final: 0.6359 (m-30) REVERT: A 190 MET cc_start: 0.8203 (ptp) cc_final: 0.7834 (ptp) REVERT: A 193 PHE cc_start: 0.8942 (m-10) cc_final: 0.8534 (m-10) REVERT: A 220 MET cc_start: 0.8385 (tpt) cc_final: 0.8078 (tpt) REVERT: A 270 LYS cc_start: 0.6788 (ptpt) cc_final: 0.6177 (tmtt) REVERT: B 61 LYS cc_start: 0.3607 (tttt) cc_final: 0.3307 (tttt) REVERT: B 81 LYS cc_start: 0.9240 (tppt) cc_final: 0.8983 (mttt) REVERT: B 163 MET cc_start: 0.8608 (mmm) cc_final: 0.8250 (mmm) REVERT: B 200 GLN cc_start: 0.8403 (mp10) cc_final: 0.7613 (tp40) REVERT: B 270 LYS cc_start: 0.7523 (pttt) cc_final: 0.7107 (tptp) REVERT: C 154 ARG cc_start: 0.8849 (mmt-90) cc_final: 0.8647 (mmt180) REVERT: C 169 PHE cc_start: 0.8917 (t80) cc_final: 0.8690 (t80) REVERT: C 235 PHE cc_start: 0.8653 (t80) cc_final: 0.8305 (m-80) REVERT: C 245 GLN cc_start: 0.8463 (mm-40) cc_final: 0.8201 (mm-40) REVERT: C 248 ASP cc_start: 0.8585 (m-30) cc_final: 0.8295 (t70) REVERT: C 252 GLN cc_start: 0.8652 (mt0) cc_final: 0.8123 (mt0) REVERT: D 169 PHE cc_start: 0.8843 (t80) cc_final: 0.8467 (t80) REVERT: E 140 ASP cc_start: 0.7736 (t0) cc_final: 0.7504 (t0) REVERT: E 237 ARG cc_start: 0.8598 (mmt180) cc_final: 0.8068 (mmt180) REVERT: F 34 PHE cc_start: 0.4517 (m-80) cc_final: 0.4202 (m-80) REVERT: F 35 MET cc_start: 0.2684 (tpt) cc_final: 0.2155 (mmm) REVERT: G 27 MET cc_start: 0.8719 (mmm) cc_final: 0.8421 (mpp) REVERT: G 35 MET cc_start: 0.8038 (mtt) cc_final: 0.7758 (mmm) outliers start: 26 outliers final: 20 residues processed: 239 average time/residue: 0.2033 time to fit residues: 67.3517 Evaluate side-chains 233 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 213 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 150 PHE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 75 TRP Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 245 GLN Chi-restraints excluded: chain E residue 185 THR Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain G residue 21 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 54 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 7 optimal weight: 7.9990 chunk 84 optimal weight: 3.9990 chunk 17 optimal weight: 0.0040 chunk 91 optimal weight: 20.0000 chunk 5 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 139 ASN ** C 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 GLN E 257 GLN ** E 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.077790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.063713 restraints weight = 47240.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.064914 restraints weight = 34914.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.065756 restraints weight = 27453.759| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9340 Z= 0.157 Angle : 0.744 12.119 12657 Z= 0.371 Chirality : 0.043 0.213 1502 Planarity : 0.004 0.028 1642 Dihedral : 4.361 24.068 1320 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.00 % Allowed : 24.20 % Favored : 72.81 % 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: 1.03 (0.25), residues: 1208 helix: 1.32 (0.16), residues: 1028 sheet: None (None), residues: 0 loop : -2.95 (0.42), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 75 HIS 0.005 0.001 HIS C 242 PHE 0.043 0.002 PHE B 79 TYR 0.016 0.002 TYR C 232 ARG 0.003 0.000 ARG B 90 Details of bonding type rmsd hydrogen bonds : bond 0.03746 ( 865) hydrogen bonds : angle 4.38865 ( 2589) covalent geometry : bond 0.00316 ( 9340) covalent geometry : angle 0.74370 (12657) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 228 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.9294 (pttp) cc_final: 0.8990 (tppt) REVERT: A 126 ASN cc_start: 0.8930 (t0) cc_final: 0.8311 (p0) REVERT: A 140 ASP cc_start: 0.7086 (m-30) cc_final: 0.6567 (m-30) REVERT: A 190 MET cc_start: 0.8214 (ptp) cc_final: 0.7615 (ptp) REVERT: A 193 PHE cc_start: 0.8924 (m-10) cc_final: 0.8503 (m-10) REVERT: A 220 MET cc_start: 0.8418 (tpt) cc_final: 0.8141 (tpt) REVERT: B 61 LYS cc_start: 0.3813 (tttt) cc_final: 0.3499 (tttt) REVERT: B 75 TRP cc_start: 0.8312 (m-10) cc_final: 0.8075 (m100) REVERT: B 81 LYS cc_start: 0.9271 (tppt) cc_final: 0.9003 (mttt) REVERT: B 163 MET cc_start: 0.8661 (mmm) cc_final: 0.8306 (mmm) REVERT: B 200 GLN cc_start: 0.8436 (mp10) cc_final: 0.7641 (tp40) REVERT: B 270 LYS cc_start: 0.7419 (pttt) cc_final: 0.7051 (tptp) REVERT: C 169 PHE cc_start: 0.8973 (t80) cc_final: 0.8730 (t80) REVERT: C 179 PHE cc_start: 0.8947 (m-10) cc_final: 0.8713 (m-80) REVERT: C 232 TYR cc_start: 0.8024 (t80) cc_final: 0.7820 (t80) REVERT: C 235 PHE cc_start: 0.8750 (t80) cc_final: 0.8352 (m-80) REVERT: C 245 GLN cc_start: 0.8550 (mm-40) cc_final: 0.8264 (mm-40) REVERT: C 248 ASP cc_start: 0.8626 (m-30) cc_final: 0.8350 (t70) REVERT: C 252 GLN cc_start: 0.8676 (mt0) cc_final: 0.8137 (mt0) REVERT: C 277 GLN cc_start: 0.5863 (OUTLIER) cc_final: 0.5552 (pm20) REVERT: D 220 MET cc_start: 0.9364 (mmm) cc_final: 0.8711 (mpp) REVERT: E 150 PHE cc_start: 0.8640 (OUTLIER) cc_final: 0.8423 (t80) REVERT: E 237 ARG cc_start: 0.8585 (mmt180) cc_final: 0.8222 (tpt90) REVERT: F 34 PHE cc_start: 0.4585 (m-80) cc_final: 0.4296 (m-80) REVERT: F 35 MET cc_start: 0.2782 (tpt) cc_final: 0.2313 (mmm) outliers start: 28 outliers final: 21 residues processed: 244 average time/residue: 0.2129 time to fit residues: 72.7675 Evaluate side-chains 233 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 210 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 150 PHE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 245 GLN Chi-restraints excluded: chain E residue 150 PHE Chi-restraints excluded: chain E residue 185 THR Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain G residue 21 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 64 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 112 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 chunk 107 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 GLN ** E 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.078436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.064388 restraints weight = 47463.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.065720 restraints weight = 34695.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.066639 restraints weight = 27304.429| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9340 Z= 0.141 Angle : 0.759 12.519 12657 Z= 0.376 Chirality : 0.043 0.217 1502 Planarity : 0.003 0.026 1642 Dihedral : 4.328 23.534 1320 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.68 % Allowed : 25.91 % Favored : 71.41 % 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: 1.15 (0.25), residues: 1208 helix: 1.40 (0.16), residues: 1027 sheet: None (None), residues: 0 loop : -2.89 (0.42), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 187 HIS 0.005 0.001 HIS E 242 PHE 0.048 0.002 PHE A 235 TYR 0.014 0.002 TYR D 232 ARG 0.008 0.000 ARG A 165 Details of bonding type rmsd hydrogen bonds : bond 0.03688 ( 865) hydrogen bonds : angle 4.35746 ( 2589) covalent geometry : bond 0.00290 ( 9340) covalent geometry : angle 0.75884 (12657) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 227 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 ASN cc_start: 0.8936 (t0) cc_final: 0.8310 (p0) REVERT: A 140 ASP cc_start: 0.7087 (m-30) cc_final: 0.6547 (m-30) REVERT: A 190 MET cc_start: 0.8218 (ptp) cc_final: 0.7629 (ptp) REVERT: A 193 PHE cc_start: 0.8877 (m-10) cc_final: 0.8567 (m-10) REVERT: A 220 MET cc_start: 0.8419 (tpt) cc_final: 0.8120 (tpt) REVERT: A 270 LYS cc_start: 0.5970 (mttt) cc_final: 0.5449 (tmtt) REVERT: B 81 LYS cc_start: 0.9284 (tppt) cc_final: 0.8970 (mttt) REVERT: B 163 MET cc_start: 0.8804 (mmm) cc_final: 0.8388 (mmm) REVERT: B 200 GLN cc_start: 0.8447 (mp10) cc_final: 0.7685 (tp40) REVERT: B 220 MET cc_start: 0.8915 (mtp) cc_final: 0.8658 (mtm) REVERT: B 270 LYS cc_start: 0.7528 (pttt) cc_final: 0.7084 (tptp) REVERT: C 154 ARG cc_start: 0.8886 (mmt-90) cc_final: 0.8509 (mmm-85) REVERT: C 169 PHE cc_start: 0.8976 (t80) cc_final: 0.8715 (t80) REVERT: C 179 PHE cc_start: 0.8932 (m-10) cc_final: 0.8674 (m-80) REVERT: C 232 TYR cc_start: 0.8051 (t80) cc_final: 0.7757 (t80) REVERT: C 235 PHE cc_start: 0.8806 (t80) cc_final: 0.8393 (m-80) REVERT: C 245 GLN cc_start: 0.8629 (mm-40) cc_final: 0.8316 (mm-40) REVERT: C 248 ASP cc_start: 0.8632 (m-30) cc_final: 0.8322 (t70) REVERT: C 252 GLN cc_start: 0.8781 (mt0) cc_final: 0.8202 (mt0) REVERT: C 277 GLN cc_start: 0.5846 (OUTLIER) cc_final: 0.5588 (pm20) REVERT: D 220 MET cc_start: 0.9355 (mmm) cc_final: 0.8709 (mpp) REVERT: E 140 ASP cc_start: 0.8002 (t0) cc_final: 0.7563 (t0) REVERT: E 237 ARG cc_start: 0.8534 (mmt180) cc_final: 0.8156 (tpt90) outliers start: 25 outliers final: 21 residues processed: 242 average time/residue: 0.2060 time to fit residues: 69.4162 Evaluate side-chains 235 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 213 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 150 PHE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 75 TRP Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 245 GLN Chi-restraints excluded: chain E residue 185 THR Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain G residue 21 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 80 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 14 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 41 optimal weight: 0.2980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 GLN ** E 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.078488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.064364 restraints weight = 47768.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.065683 restraints weight = 34895.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.066571 restraints weight = 27282.270| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9340 Z= 0.144 Angle : 0.782 13.301 12657 Z= 0.387 Chirality : 0.044 0.253 1502 Planarity : 0.004 0.027 1642 Dihedral : 4.318 23.471 1320 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.21 % Allowed : 26.34 % Favored : 70.45 % 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: 1.13 (0.24), residues: 1208 helix: 1.37 (0.16), residues: 1027 sheet: None (None), residues: 0 loop : -2.84 (0.42), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 75 HIS 0.005 0.001 HIS C 242 PHE 0.044 0.002 PHE B 79 TYR 0.015 0.002 TYR D 232 ARG 0.003 0.000 ARG C 165 Details of bonding type rmsd hydrogen bonds : bond 0.03721 ( 865) hydrogen bonds : angle 4.39449 ( 2589) covalent geometry : bond 0.00296 ( 9340) covalent geometry : angle 0.78237 (12657) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 220 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.9288 (pttp) cc_final: 0.8981 (tppt) REVERT: A 126 ASN cc_start: 0.8920 (t0) cc_final: 0.8306 (p0) REVERT: A 140 ASP cc_start: 0.6978 (m-30) cc_final: 0.6452 (m-30) REVERT: A 190 MET cc_start: 0.8311 (ptp) cc_final: 0.7670 (ptp) REVERT: A 193 PHE cc_start: 0.8912 (m-10) cc_final: 0.8565 (m-10) REVERT: A 220 MET cc_start: 0.8408 (tpt) cc_final: 0.8127 (tpt) REVERT: A 237 ARG cc_start: 0.9086 (OUTLIER) cc_final: 0.8723 (ptm160) REVERT: A 270 LYS cc_start: 0.5932 (mttt) cc_final: 0.5518 (tmtt) REVERT: B 75 TRP cc_start: 0.8517 (m-10) cc_final: 0.8269 (m100) REVERT: B 81 LYS cc_start: 0.9314 (tppt) cc_final: 0.9001 (mttt) REVERT: B 163 MET cc_start: 0.8747 (mmm) cc_final: 0.8297 (mmm) REVERT: B 200 GLN cc_start: 0.8373 (mp10) cc_final: 0.7635 (tp40) REVERT: B 220 MET cc_start: 0.8939 (mtp) cc_final: 0.8676 (mtm) REVERT: B 270 LYS cc_start: 0.7531 (pttt) cc_final: 0.7093 (tptp) REVERT: C 92 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8475 (pp) REVERT: C 154 ARG cc_start: 0.8760 (mmt-90) cc_final: 0.8461 (mmm-85) REVERT: C 169 PHE cc_start: 0.8963 (t80) cc_final: 0.8742 (t80) REVERT: C 179 PHE cc_start: 0.8852 (m-10) cc_final: 0.8633 (m-80) REVERT: C 232 TYR cc_start: 0.7999 (t80) cc_final: 0.7741 (t80) REVERT: C 235 PHE cc_start: 0.8787 (t80) cc_final: 0.8346 (m-80) REVERT: C 248 ASP cc_start: 0.8674 (m-30) cc_final: 0.8392 (t70) REVERT: C 252 GLN cc_start: 0.8792 (mt0) cc_final: 0.8212 (mt0) REVERT: C 277 GLN cc_start: 0.5756 (OUTLIER) cc_final: 0.5435 (pm20) REVERT: D 220 MET cc_start: 0.9299 (mmm) cc_final: 0.8676 (mpp) REVERT: D 237 ARG cc_start: 0.8985 (ttm170) cc_final: 0.8710 (ttm170) REVERT: E 52 MET cc_start: 0.5936 (mmp) cc_final: 0.5372 (mmp) REVERT: E 140 ASP cc_start: 0.7996 (t0) cc_final: 0.7607 (t0) REVERT: E 216 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8584 (tt) REVERT: E 237 ARG cc_start: 0.8531 (mmt180) cc_final: 0.8155 (tpt90) REVERT: E 270 LYS cc_start: 0.7296 (pptt) cc_final: 0.6469 (pttt) REVERT: F 35 MET cc_start: 0.2967 (tpt) cc_final: 0.2191 (tpt) outliers start: 30 outliers final: 22 residues processed: 240 average time/residue: 0.2308 time to fit residues: 77.2343 Evaluate side-chains 239 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 213 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 150 PHE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 75 TRP Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 245 GLN Chi-restraints excluded: chain E residue 185 THR Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain G residue 21 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 83 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 97 optimal weight: 9.9990 chunk 9 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 GLN ** E 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.078194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.064233 restraints weight = 48017.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.065554 restraints weight = 34661.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.066476 restraints weight = 27104.346| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9340 Z= 0.149 Angle : 0.809 14.169 12657 Z= 0.403 Chirality : 0.045 0.224 1502 Planarity : 0.005 0.102 1642 Dihedral : 4.353 23.411 1320 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.43 % Allowed : 26.23 % Favored : 70.34 % 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: 1.11 (0.25), residues: 1208 helix: 1.35 (0.16), residues: 1027 sheet: None (None), residues: 0 loop : -2.80 (0.42), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 187 HIS 0.004 0.001 HIS B 242 PHE 0.049 0.002 PHE A 235 TYR 0.016 0.002 TYR D 232 ARG 0.021 0.000 ARG E 154 Details of bonding type rmsd hydrogen bonds : bond 0.03814 ( 865) hydrogen bonds : angle 4.41762 ( 2589) covalent geometry : bond 0.00306 ( 9340) covalent geometry : angle 0.80943 (12657) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 219 time to evaluate : 1.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.9286 (pttp) cc_final: 0.8962 (tppt) REVERT: A 126 ASN cc_start: 0.8838 (t0) cc_final: 0.8236 (p0) REVERT: A 140 ASP cc_start: 0.6815 (m-30) cc_final: 0.6332 (m-30) REVERT: A 190 MET cc_start: 0.8341 (ptp) cc_final: 0.7675 (ptp) REVERT: A 193 PHE cc_start: 0.8954 (m-10) cc_final: 0.8550 (m-10) REVERT: A 220 MET cc_start: 0.8375 (tpt) cc_final: 0.8111 (tpt) REVERT: A 237 ARG cc_start: 0.9027 (OUTLIER) cc_final: 0.8628 (ptm160) REVERT: A 270 LYS cc_start: 0.5944 (mttt) cc_final: 0.5649 (tmtt) REVERT: B 81 LYS cc_start: 0.9302 (tppt) cc_final: 0.8800 (mttt) REVERT: B 163 MET cc_start: 0.8669 (mmm) cc_final: 0.8079 (mmm) REVERT: B 200 GLN cc_start: 0.8354 (mp10) cc_final: 0.7637 (tp40) REVERT: B 220 MET cc_start: 0.8886 (mtp) cc_final: 0.8683 (mtm) REVERT: B 270 LYS cc_start: 0.7570 (pttt) cc_final: 0.7132 (tptp) REVERT: C 169 PHE cc_start: 0.8916 (t80) cc_final: 0.8685 (t80) REVERT: C 232 TYR cc_start: 0.7913 (t80) cc_final: 0.7621 (t80) REVERT: C 235 PHE cc_start: 0.8645 (t80) cc_final: 0.8219 (m-80) REVERT: C 248 ASP cc_start: 0.8655 (m-30) cc_final: 0.8353 (t70) REVERT: C 252 GLN cc_start: 0.8659 (mt0) cc_final: 0.8179 (mt0) REVERT: C 277 GLN cc_start: 0.5629 (OUTLIER) cc_final: 0.5368 (pm20) REVERT: D 220 MET cc_start: 0.9274 (mmm) cc_final: 0.8691 (mpp) REVERT: D 237 ARG cc_start: 0.8881 (ttm170) cc_final: 0.8602 (ttm170) REVERT: E 52 MET cc_start: 0.6029 (mmp) cc_final: 0.5442 (mmp) REVERT: E 216 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8538 (tt) REVERT: E 237 ARG cc_start: 0.8521 (mmt180) cc_final: 0.8191 (tpt90) REVERT: E 270 LYS cc_start: 0.7347 (pptt) cc_final: 0.6778 (pttt) REVERT: F 35 MET cc_start: 0.1828 (tpt) cc_final: 0.1291 (tpt) outliers start: 32 outliers final: 25 residues processed: 239 average time/residue: 0.2683 time to fit residues: 89.3914 Evaluate side-chains 238 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 210 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 150 PHE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 75 TRP Chi-restraints excluded: chain C residue 191 ASN Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 245 GLN Chi-restraints excluded: chain E residue 150 PHE Chi-restraints excluded: chain E residue 185 THR Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain G residue 21 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 15 optimal weight: 9.9990 chunk 34 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 115 optimal weight: 0.4980 chunk 99 optimal weight: 0.0770 chunk 61 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 38 optimal weight: 0.2980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 GLN ** E 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.079313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.065098 restraints weight = 47525.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.066426 restraints weight = 34595.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.067384 restraints weight = 27490.815| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9340 Z= 0.148 Angle : 0.862 16.054 12657 Z= 0.419 Chirality : 0.046 0.227 1502 Planarity : 0.004 0.036 1642 Dihedral : 4.346 22.866 1320 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 16.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.78 % Allowed : 27.41 % Favored : 69.81 % 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: 1.11 (0.25), residues: 1208 helix: 1.34 (0.16), residues: 1027 sheet: None (None), residues: 0 loop : -2.70 (0.42), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 75 HIS 0.005 0.001 HIS C 274 PHE 0.047 0.003 PHE B 79 TYR 0.017 0.002 TYR D 232 ARG 0.010 0.000 ARG E 154 Details of bonding type rmsd hydrogen bonds : bond 0.03840 ( 865) hydrogen bonds : angle 4.39249 ( 2589) covalent geometry : bond 0.00304 ( 9340) covalent geometry : angle 0.86190 (12657) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 223 time to evaluate : 1.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.9252 (pttp) cc_final: 0.8916 (tppt) REVERT: A 81 LYS cc_start: 0.8438 (mtmt) cc_final: 0.8180 (mttt) REVERT: A 106 ASP cc_start: 0.8290 (m-30) cc_final: 0.7867 (p0) REVERT: A 126 ASN cc_start: 0.8884 (t0) cc_final: 0.8300 (p0) REVERT: A 140 ASP cc_start: 0.6789 (m-30) cc_final: 0.6308 (m-30) REVERT: A 190 MET cc_start: 0.8365 (ptp) cc_final: 0.7777 (ptt) REVERT: A 193 PHE cc_start: 0.8940 (m-10) cc_final: 0.8324 (m-80) REVERT: A 220 MET cc_start: 0.8287 (tpt) cc_final: 0.8059 (tpt) REVERT: A 237 ARG cc_start: 0.9008 (OUTLIER) cc_final: 0.8582 (ptm160) REVERT: A 270 LYS cc_start: 0.6109 (mttt) cc_final: 0.5852 (tmtt) REVERT: B 81 LYS cc_start: 0.9302 (tppt) cc_final: 0.9015 (mttt) REVERT: B 163 MET cc_start: 0.8651 (mmm) cc_final: 0.8157 (mmm) REVERT: B 200 GLN cc_start: 0.8325 (mp10) cc_final: 0.7573 (tp40) REVERT: B 220 MET cc_start: 0.8905 (mtp) cc_final: 0.8701 (mtm) REVERT: B 270 LYS cc_start: 0.7542 (pttt) cc_final: 0.7135 (tptp) REVERT: C 64 MET cc_start: 0.7152 (tpp) cc_final: 0.6773 (mmp) REVERT: C 65 ILE cc_start: 0.8554 (mm) cc_final: 0.8221 (pt) REVERT: C 113 GLN cc_start: 0.8043 (tm-30) cc_final: 0.7735 (tm-30) REVERT: C 169 PHE cc_start: 0.8926 (t80) cc_final: 0.8678 (t80) REVERT: C 248 ASP cc_start: 0.8556 (m-30) cc_final: 0.8309 (t70) REVERT: C 252 GLN cc_start: 0.8645 (mt0) cc_final: 0.8188 (mt0) REVERT: C 277 GLN cc_start: 0.5560 (OUTLIER) cc_final: 0.5243 (pm20) REVERT: D 220 MET cc_start: 0.9253 (mmm) cc_final: 0.8698 (mpp) REVERT: D 237 ARG cc_start: 0.8897 (ttm170) cc_final: 0.8600 (ttm170) REVERT: E 52 MET cc_start: 0.6083 (mmp) cc_final: 0.5785 (mmp) REVERT: E 237 ARG cc_start: 0.8501 (mmt180) cc_final: 0.8142 (tpt90) REVERT: E 270 LYS cc_start: 0.7320 (pptt) cc_final: 0.6612 (pttt) REVERT: F 35 MET cc_start: 0.1808 (tpt) cc_final: 0.1554 (tpt) REVERT: G 34 PHE cc_start: 0.8718 (t80) cc_final: 0.8426 (t80) outliers start: 26 outliers final: 21 residues processed: 238 average time/residue: 0.2566 time to fit residues: 87.0457 Evaluate side-chains 234 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 211 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 150 PHE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain C residue 75 TRP Chi-restraints excluded: chain C residue 191 ASN Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain E residue 185 THR Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain G residue 21 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 72 optimal weight: 4.9990 chunk 105 optimal weight: 0.5980 chunk 87 optimal weight: 1.9990 chunk 19 optimal weight: 0.0770 chunk 14 optimal weight: 9.9990 chunk 113 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 97 optimal weight: 9.9990 overall best weight: 1.3344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 GLN ** E 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.078605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.064581 restraints weight = 48641.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.065885 restraints weight = 35434.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.066829 restraints weight = 27619.469| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9340 Z= 0.159 Angle : 0.905 19.314 12657 Z= 0.438 Chirality : 0.048 0.303 1502 Planarity : 0.004 0.040 1642 Dihedral : 4.392 23.396 1320 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.36 % Allowed : 28.80 % Favored : 68.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.24), residues: 1208 helix: 1.26 (0.16), residues: 1028 sheet: None (None), residues: 0 loop : -2.69 (0.42), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 75 HIS 0.005 0.001 HIS C 274 PHE 0.050 0.003 PHE A 235 TYR 0.024 0.002 TYR C 232 ARG 0.008 0.000 ARG E 154 Details of bonding type rmsd hydrogen bonds : bond 0.03945 ( 865) hydrogen bonds : angle 4.54372 ( 2589) covalent geometry : bond 0.00328 ( 9340) covalent geometry : angle 0.90467 (12657) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 216 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.9277 (pttp) cc_final: 0.8958 (tppt) REVERT: A 81 LYS cc_start: 0.8500 (mtmt) cc_final: 0.8211 (mttt) REVERT: A 106 ASP cc_start: 0.8292 (m-30) cc_final: 0.7863 (p0) REVERT: A 126 ASN cc_start: 0.8892 (t0) cc_final: 0.8293 (p0) REVERT: A 140 ASP cc_start: 0.6814 (m-30) cc_final: 0.6338 (m-30) REVERT: A 190 MET cc_start: 0.8396 (ptp) cc_final: 0.7794 (ptt) REVERT: A 193 PHE cc_start: 0.8961 (m-10) cc_final: 0.8336 (m-80) REVERT: A 220 MET cc_start: 0.8271 (tpt) cc_final: 0.8040 (tpt) REVERT: A 237 ARG cc_start: 0.9037 (OUTLIER) cc_final: 0.8555 (ptm160) REVERT: B 81 LYS cc_start: 0.9299 (tppt) cc_final: 0.9073 (mttt) REVERT: B 163 MET cc_start: 0.8630 (mmm) cc_final: 0.8183 (mmm) REVERT: B 200 GLN cc_start: 0.8334 (mp10) cc_final: 0.7530 (tp40) REVERT: B 220 MET cc_start: 0.8931 (mtp) cc_final: 0.8720 (mtm) REVERT: B 270 LYS cc_start: 0.7499 (pttt) cc_final: 0.7108 (tptp) REVERT: C 64 MET cc_start: 0.6707 (tpp) cc_final: 0.6434 (mmp) REVERT: C 65 ILE cc_start: 0.8672 (mm) cc_final: 0.8314 (pt) REVERT: C 169 PHE cc_start: 0.8916 (t80) cc_final: 0.8672 (t80) REVERT: C 248 ASP cc_start: 0.8543 (m-30) cc_final: 0.8284 (t70) REVERT: C 252 GLN cc_start: 0.8629 (mt0) cc_final: 0.8190 (mt0) REVERT: D 220 MET cc_start: 0.9222 (mmm) cc_final: 0.8686 (mpp) REVERT: E 237 ARG cc_start: 0.8419 (mmt180) cc_final: 0.8107 (tpt90) REVERT: E 270 LYS cc_start: 0.7260 (pptt) cc_final: 0.6690 (pttt) REVERT: F 35 MET cc_start: 0.2282 (tpt) cc_final: 0.1871 (tpt) REVERT: G 34 PHE cc_start: 0.8771 (t80) cc_final: 0.8437 (t80) outliers start: 22 outliers final: 19 residues processed: 226 average time/residue: 0.2009 time to fit residues: 63.7087 Evaluate side-chains 229 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 209 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 150 PHE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain C residue 75 TRP Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain E residue 185 THR Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain F residue 23 PHE Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain G residue 21 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 12 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 60 optimal weight: 4.9990 chunk 104 optimal weight: 7.9990 chunk 94 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 276 HIS ** 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 = 0.3823 r_free = 0.3823 target = 0.078450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.064335 restraints weight = 48433.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.065673 restraints weight = 35342.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.066588 restraints weight = 27581.893| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9340 Z= 0.164 Angle : 0.916 18.183 12657 Z= 0.446 Chirality : 0.047 0.271 1502 Planarity : 0.004 0.044 1642 Dihedral : 4.413 24.138 1320 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.46 % Allowed : 28.80 % Favored : 68.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.00 (0.24), residues: 1208 helix: 1.26 (0.16), residues: 1027 sheet: None (None), residues: 0 loop : -2.67 (0.42), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 187 HIS 0.004 0.001 HIS A 55 PHE 0.050 0.003 PHE B 79 TYR 0.029 0.002 TYR C 232 ARG 0.007 0.000 ARG E 154 Details of bonding type rmsd hydrogen bonds : bond 0.03990 ( 865) hydrogen bonds : angle 4.57011 ( 2589) covalent geometry : bond 0.00338 ( 9340) covalent geometry : angle 0.91557 (12657) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3289.69 seconds wall clock time: 60 minutes 3.81 seconds (3603.81 seconds total)