Starting phenix.real_space_refine on Sat Apr 4 21:26:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m9q_63737/04_2026/9m9q_63737.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m9q_63737/04_2026/9m9q_63737.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9m9q_63737/04_2026/9m9q_63737.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m9q_63737/04_2026/9m9q_63737.map" model { file = "/net/cci-nas-00/data/ceres_data/9m9q_63737/04_2026/9m9q_63737.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m9q_63737/04_2026/9m9q_63737.cif" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 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: 7 Type Number sf(0) Gaussians Br 2 7.06 5 S 26 5.16 5 Cl 2 4.86 5 C 2553 2.51 5 N 630 2.21 5 O 676 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3895 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1912 Classifications: {'peptide': 246} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 241} Chain breaks: 1 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'TRP:plan': 1, 'PHE:plan': 1, 'ARG:plan': 3, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "B" Number of atoms: 1969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1969 Classifications: {'peptide': 251} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 246} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 33 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'HLT': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'HLT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.11, per 1000 atoms: 0.28 Number of scatterers: 3895 At special positions: 0 Unit cell: (64.64, 67.872, 81.608, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Br 2 34.99 Cl 2 17.00 S 26 16.00 F 6 9.00 O 676 8.00 N 630 7.00 C 2553 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.24 Conformation dependent library (CDL) restraints added in 109.6 milliseconds 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 922 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 0 sheets defined 81.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 17 through 25 removed outlier: 3.856A pdb=" N LEU A 21 " --> pdb=" O ASN A 17 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A 23 " --> pdb=" O ARG A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 42 Processing helix chain 'A' and resid 45 through 64 removed outlier: 3.639A pdb=" N HIS A 64 " --> pdb=" O PHE A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 85 Processing helix chain 'A' and resid 96 through 109 removed outlier: 3.573A pdb=" N TYR A 102 " --> pdb=" O THR A 98 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N PHE A 103 " --> pdb=" O GLY A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 160 removed outlier: 4.034A pdb=" N ILE A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE A 129 " --> pdb=" O ILE A 125 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU A 147 " --> pdb=" O ASN A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 220 Proline residue: A 218 - end of helix Processing helix chain 'A' and resid 223 through 236 Processing helix chain 'A' and resid 253 through 292 removed outlier: 4.038A pdb=" N GLN A 285 " --> pdb=" O ILE A 281 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ASN A 288 " --> pdb=" O LYS A 284 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N TRP A 289 " --> pdb=" O GLN A 285 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE A 290 " --> pdb=" O SER A 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 37 Processing helix chain 'B' and resid 37 through 64 removed outlier: 3.966A pdb=" N ALA B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N HIS B 45 " --> pdb=" O LEU B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 84 Processing helix chain 'B' and resid 96 through 109 Processing helix chain 'B' and resid 120 through 163 removed outlier: 3.745A pdb=" N ILE B 125 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N PHE B 126 " --> pdb=" O GLY B 122 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE B 129 " --> pdb=" O ILE B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 220 Proline residue: B 218 - end of helix Processing helix chain 'B' and resid 223 through 236 Processing helix chain 'B' and resid 253 through 287 removed outlier: 3.601A pdb=" N TYR B 257 " --> pdb=" O SER B 253 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG B 258 " --> pdb=" O GLN B 254 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N PHE B 259 " --> pdb=" O GLY B 255 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLN B 285 " --> pdb=" O ILE B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 290 No H-bonds generated for 'chain 'B' and resid 288 through 290' 308 hydrogen bonds defined for protein. 924 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.57 Time building geometry restraints manager: 0.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.35: 1196 1.35 - 1.50: 1148 1.50 - 1.66: 1601 1.66 - 1.82: 36 1.82 - 1.98: 4 Bond restraints: 3985 Sorted by residual: bond pdb=" CZ ARG A 92 " pdb=" NH2 ARG A 92 " ideal model delta sigma weight residual 1.330 1.293 0.037 1.30e-02 5.92e+03 8.18e+00 bond pdb=" CZ ARG B 52 " pdb=" NH2 ARG B 52 " ideal model delta sigma weight residual 1.330 1.294 0.036 1.30e-02 5.92e+03 7.60e+00 bond pdb=" CD GLN B 247 " pdb=" NE2 GLN B 247 " ideal model delta sigma weight residual 1.328 1.270 0.058 2.10e-02 2.27e+03 7.56e+00 bond pdb=" CZ ARG B 76 " pdb=" NH2 ARG B 76 " ideal model delta sigma weight residual 1.330 1.294 0.036 1.30e-02 5.92e+03 7.46e+00 bond pdb=" CZ ARG B 83 " pdb=" NH2 ARG B 83 " ideal model delta sigma weight residual 1.330 1.296 0.034 1.30e-02 5.92e+03 7.02e+00 ... (remaining 3980 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 4001 1.89 - 3.78: 1145 3.78 - 5.67: 220 5.67 - 7.57: 34 7.57 - 9.46: 3 Bond angle restraints: 5403 Sorted by residual: angle pdb=" CA PHE B 235 " pdb=" CB PHE B 235 " pdb=" CG PHE B 235 " ideal model delta sigma weight residual 113.80 121.03 -7.23 1.00e+00 1.00e+00 5.22e+01 angle pdb=" CA ASP A 226 " pdb=" CB ASP A 226 " pdb=" CG ASP A 226 " ideal model delta sigma weight residual 112.60 119.59 -6.99 1.00e+00 1.00e+00 4.89e+01 angle pdb=" CA PHE B 141 " pdb=" CB PHE B 141 " pdb=" CG PHE B 141 " ideal model delta sigma weight residual 113.80 120.49 -6.69 1.00e+00 1.00e+00 4.47e+01 angle pdb=" CA PHE A 235 " pdb=" CB PHE A 235 " pdb=" CG PHE A 235 " ideal model delta sigma weight residual 113.80 120.45 -6.65 1.00e+00 1.00e+00 4.42e+01 angle pdb=" CA PHE B 240 " pdb=" CB PHE B 240 " pdb=" CG PHE B 240 " ideal model delta sigma weight residual 113.80 120.07 -6.27 1.00e+00 1.00e+00 3.93e+01 ... (remaining 5398 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.92: 1972 14.92 - 29.83: 245 29.83 - 44.75: 56 44.75 - 59.67: 13 59.67 - 74.59: 4 Dihedral angle restraints: 2290 sinusoidal: 849 harmonic: 1441 Sorted by residual: dihedral pdb=" CA TRP B 95 " pdb=" C TRP B 95 " pdb=" N ASP B 96 " pdb=" CA ASP B 96 " ideal model delta harmonic sigma weight residual 180.00 149.14 30.86 0 5.00e+00 4.00e-02 3.81e+01 dihedral pdb=" C THR A 110 " pdb=" N THR A 110 " pdb=" CA THR A 110 " pdb=" CB THR A 110 " ideal model delta harmonic sigma weight residual -122.00 -136.91 14.91 0 2.50e+00 1.60e-01 3.56e+01 dihedral pdb=" C VAL A 88 " pdb=" N VAL A 88 " pdb=" CA VAL A 88 " pdb=" CB VAL A 88 " ideal model delta harmonic sigma weight residual -122.00 -136.15 14.15 0 2.50e+00 1.60e-01 3.20e+01 ... (remaining 2287 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 502 0.112 - 0.224: 99 0.224 - 0.336: 9 0.336 - 0.448: 4 0.448 - 0.560: 3 Chirality restraints: 617 Sorted by residual: chirality pdb=" CA THR A 110 " pdb=" N THR A 110 " pdb=" C THR A 110 " pdb=" CB THR A 110 " both_signs ideal model delta sigma weight residual False 2.53 1.97 0.56 2.00e-01 2.50e+01 7.83e+00 chirality pdb=" CA THR B 110 " pdb=" N THR B 110 " pdb=" C THR B 110 " pdb=" CB THR B 110 " both_signs ideal model delta sigma weight residual False 2.53 2.05 0.48 2.00e-01 2.50e+01 5.74e+00 chirality pdb=" CA VAL A 88 " pdb=" N VAL A 88 " pdb=" C VAL A 88 " pdb=" CB VAL A 88 " both_signs ideal model delta sigma weight residual False 2.44 1.98 0.46 2.00e-01 2.50e+01 5.29e+00 ... (remaining 614 not shown) Planarity restraints: 667 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 30 " -0.140 2.00e-02 2.50e+03 7.47e-02 1.12e+02 pdb=" CG TYR B 30 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR B 30 " 0.063 2.00e-02 2.50e+03 pdb=" CD2 TYR B 30 " 0.068 2.00e-02 2.50e+03 pdb=" CE1 TYR B 30 " 0.040 2.00e-02 2.50e+03 pdb=" CE2 TYR B 30 " 0.035 2.00e-02 2.50e+03 pdb=" CZ TYR B 30 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR B 30 " -0.107 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 30 " -0.127 2.00e-02 2.50e+03 6.64e-02 8.83e+01 pdb=" CG TYR A 30 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR A 30 " 0.068 2.00e-02 2.50e+03 pdb=" CD2 TYR A 30 " 0.056 2.00e-02 2.50e+03 pdb=" CE1 TYR A 30 " 0.021 2.00e-02 2.50e+03 pdb=" CE2 TYR A 30 " 0.034 2.00e-02 2.50e+03 pdb=" CZ TYR A 30 " -0.014 2.00e-02 2.50e+03 pdb=" OH TYR A 30 " -0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 78 " -0.115 2.00e-02 2.50e+03 6.28e-02 7.89e+01 pdb=" CG TYR A 78 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR A 78 " 0.053 2.00e-02 2.50e+03 pdb=" CD2 TYR A 78 " 0.049 2.00e-02 2.50e+03 pdb=" CE1 TYR A 78 " 0.035 2.00e-02 2.50e+03 pdb=" CE2 TYR A 78 " 0.035 2.00e-02 2.50e+03 pdb=" CZ TYR A 78 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 78 " -0.096 2.00e-02 2.50e+03 ... (remaining 664 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 191 2.74 - 3.28: 4373 3.28 - 3.82: 6457 3.82 - 4.36: 8422 4.36 - 4.90: 13533 Nonbonded interactions: 32976 Sorted by model distance: nonbonded pdb=" OE2 GLU B 220 " pdb=" OH TYR B 257 " model vdw 2.197 3.040 nonbonded pdb=" O ALA B 58 " pdb=" OG SER B 61 " model vdw 2.249 3.040 nonbonded pdb=" OH TYR B 229 " pdb=" OD2 ASP B 242 " model vdw 2.541 3.040 nonbonded pdb=" OH TYR A 229 " pdb=" OD2 ASP A 242 " model vdw 2.545 3.040 nonbonded pdb=" O ARG B 56 " pdb=" OD1 ASN B 59 " model vdw 2.550 3.040 ... (remaining 32971 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 17 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 63 or (resid 64 and (name N or nam \ e CA or name C or name O or name CB )) or resid 65 or (resid 66 and (name N or n \ ame CA or name C or name O or name CB )) or resid 67 through 93 or (resid 94 and \ (name N or name CA or name C or name O or name CB )) or resid 95 through 290 or \ resid 501)) selection = (chain 'B' and (resid 17 through 31 or (resid 32 and (name N or name CA or name \ C or name O or name CB )) or resid 33 through 42 or (resid 43 through 46 and (na \ me N or name CA or name C or name O or name CB )) or resid 47 through 59 or (res \ id 60 and (name N or name CA or name C or name O or name CB )) or resid 61 or (r \ esid 62 and (name N or name CA or name C or name O or name CB )) or resid 63 thr \ ough 95 or (resid 96 and (name N or name CA or name C or name O or name CB )) or \ resid 97 through 160 or resid 191 through 251 or (resid 252 and (name N or name \ CA or name C or name O or name CB )) or resid 253 through 501)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.530 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5597 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 : 0.012 0.058 3985 Z= 0.712 Angle : 1.805 9.457 5403 Z= 1.230 Chirality : 0.096 0.560 617 Planarity : 0.015 0.075 667 Dihedral : 14.368 74.586 1368 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.70 % Favored : 95.09 % Rotamer: Outliers : 3.71 % Allowed : 11.14 % Favored : 85.15 % Cbeta Deviations : 1.52 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.49 (0.31), residues: 489 helix: -1.49 (0.20), residues: 370 sheet: None (None), residues: 0 loop : -1.51 (0.58), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 83 TYR 0.140 0.022 TYR B 30 PHE 0.102 0.017 PHE A 225 TRP 0.086 0.018 TRP B 95 HIS 0.006 0.002 HIS A 64 Details of bonding type rmsd covalent geometry : bond 0.01202 ( 3985) covalent geometry : angle 1.80486 ( 5403) hydrogen bonds : bond 0.14462 ( 308) hydrogen bonds : angle 8.42850 ( 924) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.137 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 GLU cc_start: 0.5795 (mp0) cc_final: 0.5522 (mp0) REVERT: A 152 ILE cc_start: 0.6624 (pp) cc_final: 0.6349 (pp) REVERT: A 222 TRP cc_start: 0.7421 (m-10) cc_final: 0.6376 (m-10) REVERT: A 269 VAL cc_start: 0.8105 (p) cc_final: 0.7794 (t) REVERT: B 90 ASN cc_start: 0.6470 (t0) cc_final: 0.6166 (t0) outliers start: 15 outliers final: 4 residues processed: 68 average time/residue: 0.2394 time to fit residues: 17.4803 Evaluate side-chains 52 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 132 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 0.5980 chunk 48 optimal weight: 0.0370 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 0.1980 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 248 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4753 r_free = 0.4753 target = 0.226229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.213245 restraints weight = 5837.801| |-----------------------------------------------------------------------------| r_work (start): 0.4629 rms_B_bonded: 2.14 r_work: 0.4526 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.4526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5589 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3985 Z= 0.177 Angle : 0.673 7.716 5403 Z= 0.371 Chirality : 0.044 0.274 617 Planarity : 0.005 0.038 667 Dihedral : 6.712 59.467 562 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.89 % Favored : 95.91 % Rotamer: Outliers : 3.22 % Allowed : 15.35 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.34), residues: 489 helix: -0.11 (0.22), residues: 380 sheet: None (None), residues: 0 loop : -1.16 (0.65), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 148 TYR 0.013 0.002 TYR A 30 PHE 0.020 0.002 PHE A 230 TRP 0.012 0.002 TRP B 95 HIS 0.001 0.000 HIS B 45 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 3985) covalent geometry : angle 0.67266 ( 5403) hydrogen bonds : bond 0.05398 ( 308) hydrogen bonds : angle 5.73288 ( 924) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 41 time to evaluate : 0.137 Fit side-chains REVERT: A 152 ILE cc_start: 0.6727 (pp) cc_final: 0.6444 (pp) REVERT: A 220 GLU cc_start: 0.6140 (OUTLIER) cc_final: 0.5567 (mm-30) REVERT: B 26 LEU cc_start: 0.5759 (mt) cc_final: 0.5458 (mp) REVERT: B 90 ASN cc_start: 0.7026 (t0) cc_final: 0.6756 (t0) outliers start: 13 outliers final: 3 residues processed: 52 average time/residue: 0.2641 time to fit residues: 14.7449 Evaluate side-chains 41 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 290 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 42 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 9 optimal weight: 0.3980 chunk 5 optimal weight: 0.0970 chunk 48 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4747 r_free = 0.4747 target = 0.226115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.213218 restraints weight = 5851.890| |-----------------------------------------------------------------------------| r_work (start): 0.4622 rms_B_bonded: 2.13 r_work: 0.4522 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.4522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5598 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3985 Z= 0.168 Angle : 0.661 8.427 5403 Z= 0.354 Chirality : 0.041 0.207 617 Planarity : 0.004 0.037 667 Dihedral : 5.228 30.281 556 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.29 % Favored : 95.50 % Rotamer: Outliers : 4.95 % Allowed : 14.36 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.35), residues: 489 helix: 0.33 (0.23), residues: 382 sheet: None (None), residues: 0 loop : -1.00 (0.67), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 87 TYR 0.018 0.002 TYR A 251 PHE 0.016 0.001 PHE A 230 TRP 0.009 0.001 TRP B 95 HIS 0.001 0.000 HIS B 250 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 3985) covalent geometry : angle 0.66070 ( 5403) hydrogen bonds : bond 0.05023 ( 308) hydrogen bonds : angle 5.39130 ( 924) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 34 time to evaluate : 0.136 Fit side-chains revert: symmetry clash REVERT: A 152 ILE cc_start: 0.6691 (pp) cc_final: 0.6476 (pp) REVERT: A 220 GLU cc_start: 0.6111 (OUTLIER) cc_final: 0.5457 (mm-30) REVERT: A 251 TYR cc_start: 0.3833 (m-80) cc_final: 0.3616 (m-80) REVERT: B 26 LEU cc_start: 0.5890 (mt) cc_final: 0.5601 (mt) REVERT: B 90 ASN cc_start: 0.6987 (t0) cc_final: 0.6722 (t0) REVERT: B 290 ILE cc_start: 0.0719 (OUTLIER) cc_final: 0.0079 (pt) outliers start: 20 outliers final: 5 residues processed: 46 average time/residue: 0.2808 time to fit residues: 13.8691 Evaluate side-chains 41 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 290 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 48 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 39 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4735 r_free = 0.4735 target = 0.224865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.211442 restraints weight = 5895.293| |-----------------------------------------------------------------------------| r_work (start): 0.4605 rms_B_bonded: 2.16 r_work: 0.4503 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.4503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5656 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3985 Z= 0.181 Angle : 0.633 7.660 5403 Z= 0.347 Chirality : 0.041 0.215 617 Planarity : 0.004 0.035 667 Dihedral : 5.100 29.709 555 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 4.46 % Allowed : 15.35 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.36), residues: 489 helix: 0.52 (0.24), residues: 384 sheet: None (None), residues: 0 loop : -0.81 (0.72), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 87 TYR 0.021 0.002 TYR B 130 PHE 0.014 0.001 PHE A 230 TRP 0.007 0.001 TRP A 95 HIS 0.001 0.000 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 3985) covalent geometry : angle 0.63348 ( 5403) hydrogen bonds : bond 0.05013 ( 308) hydrogen bonds : angle 5.26202 ( 924) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 42 time to evaluate : 0.140 Fit side-chains revert: symmetry clash REVERT: A 220 GLU cc_start: 0.6231 (OUTLIER) cc_final: 0.5636 (mm-30) REVERT: A 251 TYR cc_start: 0.4157 (m-80) cc_final: 0.3953 (m-80) REVERT: B 26 LEU cc_start: 0.6032 (mt) cc_final: 0.5732 (mt) REVERT: B 90 ASN cc_start: 0.7004 (t0) cc_final: 0.6741 (t0) REVERT: B 152 ILE cc_start: 0.6409 (pp) cc_final: 0.6199 (pp) REVERT: B 290 ILE cc_start: 0.0612 (OUTLIER) cc_final: -0.0073 (pt) outliers start: 18 outliers final: 8 residues processed: 52 average time/residue: 0.2572 time to fit residues: 14.3869 Evaluate side-chains 51 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 202 CYS Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 290 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 29 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 34 optimal weight: 5.9990 chunk 35 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 38 optimal weight: 0.4980 chunk 41 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4739 r_free = 0.4739 target = 0.225536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.212276 restraints weight = 5930.506| |-----------------------------------------------------------------------------| r_work (start): 0.4601 rms_B_bonded: 2.14 r_work: 0.4501 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.4501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5643 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3985 Z= 0.181 Angle : 0.644 7.373 5403 Z= 0.347 Chirality : 0.040 0.211 617 Planarity : 0.004 0.036 667 Dihedral : 5.118 29.055 555 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 4.70 % Allowed : 16.58 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.37), residues: 489 helix: 0.65 (0.24), residues: 384 sheet: None (None), residues: 0 loop : -0.63 (0.72), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 87 TYR 0.016 0.002 TYR B 130 PHE 0.013 0.001 PHE B 225 TRP 0.009 0.001 TRP A 95 HIS 0.002 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 3985) covalent geometry : angle 0.64380 ( 5403) hydrogen bonds : bond 0.04931 ( 308) hydrogen bonds : angle 5.24218 ( 924) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 40 time to evaluate : 0.109 Fit side-chains revert: symmetry clash REVERT: A 198 MET cc_start: 0.5982 (tpt) cc_final: 0.5696 (tpt) REVERT: A 224 TYR cc_start: 0.6688 (t80) cc_final: 0.6301 (t80) REVERT: B 26 LEU cc_start: 0.6098 (mt) cc_final: 0.5814 (mt) REVERT: B 90 ASN cc_start: 0.6888 (t0) cc_final: 0.6645 (t0) REVERT: B 246 SER cc_start: 0.7065 (p) cc_final: 0.6823 (p) REVERT: B 290 ILE cc_start: 0.0553 (OUTLIER) cc_final: -0.0185 (pt) outliers start: 19 outliers final: 12 residues processed: 49 average time/residue: 0.2531 time to fit residues: 13.3752 Evaluate side-chains 52 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 39 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 157 MET Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 290 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 46 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 33 optimal weight: 0.4980 chunk 32 optimal weight: 0.5980 chunk 39 optimal weight: 4.9990 chunk 36 optimal weight: 0.0970 chunk 24 optimal weight: 0.3980 chunk 12 optimal weight: 0.8980 chunk 2 optimal weight: 0.0980 chunk 15 optimal weight: 0.9990 overall best weight: 0.3378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4777 r_free = 0.4777 target = 0.229142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.216062 restraints weight = 5965.568| |-----------------------------------------------------------------------------| r_work (start): 0.4652 rms_B_bonded: 2.13 r_work: 0.4552 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.4552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5539 moved from start: 0.4094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3985 Z= 0.146 Angle : 0.644 12.710 5403 Z= 0.336 Chirality : 0.043 0.400 617 Planarity : 0.004 0.034 667 Dihedral : 4.906 27.942 555 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 4.21 % Allowed : 17.08 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.38), residues: 489 helix: 0.96 (0.25), residues: 384 sheet: None (None), residues: 0 loop : -0.75 (0.72), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 87 TYR 0.013 0.001 TYR B 130 PHE 0.011 0.001 PHE B 126 TRP 0.009 0.001 TRP A 95 HIS 0.003 0.001 HIS A 250 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 3985) covalent geometry : angle 0.64397 ( 5403) hydrogen bonds : bond 0.04348 ( 308) hydrogen bonds : angle 5.02744 ( 924) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 37 time to evaluate : 0.079 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 224 TYR cc_start: 0.6586 (t80) cc_final: 0.6227 (t80) REVERT: B 26 LEU cc_start: 0.5994 (mt) cc_final: 0.5689 (mt) REVERT: B 90 ASN cc_start: 0.6858 (t0) cc_final: 0.6638 (t0) outliers start: 17 outliers final: 13 residues processed: 47 average time/residue: 0.2852 time to fit residues: 14.3647 Evaluate side-chains 50 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 37 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 202 CYS Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 290 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 33 optimal weight: 0.0270 chunk 30 optimal weight: 0.2980 chunk 39 optimal weight: 0.6980 chunk 35 optimal weight: 0.4980 chunk 31 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 261 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4770 r_free = 0.4770 target = 0.228789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.215488 restraints weight = 5954.898| |-----------------------------------------------------------------------------| r_work (start): 0.4644 rms_B_bonded: 2.14 r_work: 0.4544 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.4544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5565 moved from start: 0.4280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3985 Z= 0.157 Angle : 0.651 11.463 5403 Z= 0.344 Chirality : 0.043 0.350 617 Planarity : 0.004 0.033 667 Dihedral : 4.931 27.739 555 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.96 % Allowed : 17.33 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.38), residues: 489 helix: 1.10 (0.25), residues: 381 sheet: None (None), residues: 0 loop : -0.98 (0.69), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 87 TYR 0.013 0.001 TYR B 130 PHE 0.036 0.001 PHE B 145 TRP 0.010 0.001 TRP A 95 HIS 0.001 0.000 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 3985) covalent geometry : angle 0.65072 ( 5403) hydrogen bonds : bond 0.04453 ( 308) hydrogen bonds : angle 4.99152 ( 924) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 38 time to evaluate : 0.128 Fit side-chains revert: symmetry clash REVERT: A 224 TYR cc_start: 0.6539 (t80) cc_final: 0.6213 (t80) REVERT: B 26 LEU cc_start: 0.6082 (mt) cc_final: 0.5767 (mt) REVERT: B 90 ASN cc_start: 0.6898 (t0) cc_final: 0.6692 (t0) outliers start: 16 outliers final: 13 residues processed: 47 average time/residue: 0.2590 time to fit residues: 13.0007 Evaluate side-chains 51 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 38 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 202 CYS Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain B residue 290 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 10 optimal weight: 0.1980 chunk 48 optimal weight: 0.4980 chunk 46 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 261 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4755 r_free = 0.4755 target = 0.227176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.213928 restraints weight = 5800.347| |-----------------------------------------------------------------------------| r_work (start): 0.4640 rms_B_bonded: 2.13 r_work: 0.4539 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.4539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5585 moved from start: 0.4378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 3985 Z= 0.167 Angle : 0.678 11.221 5403 Z= 0.357 Chirality : 0.043 0.341 617 Planarity : 0.004 0.036 667 Dihedral : 4.994 28.123 555 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.96 % Allowed : 16.83 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.38), residues: 489 helix: 1.01 (0.25), residues: 381 sheet: None (None), residues: 0 loop : -1.18 (0.67), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 87 TYR 0.011 0.001 TYR B 130 PHE 0.014 0.001 PHE B 126 TRP 0.010 0.001 TRP A 95 HIS 0.001 0.000 HIS A 64 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 3985) covalent geometry : angle 0.67779 ( 5403) hydrogen bonds : bond 0.04547 ( 308) hydrogen bonds : angle 5.06965 ( 924) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 37 time to evaluate : 0.120 Fit side-chains revert: symmetry clash REVERT: A 87 ARG cc_start: 0.7662 (mmt90) cc_final: 0.7403 (mmt90) REVERT: A 115 MET cc_start: 0.5875 (mmm) cc_final: 0.5569 (mmm) REVERT: A 224 TYR cc_start: 0.6543 (t80) cc_final: 0.6228 (t80) REVERT: B 26 LEU cc_start: 0.6133 (mt) cc_final: 0.5805 (mt) REVERT: B 90 ASN cc_start: 0.6952 (t0) cc_final: 0.6725 (t0) outliers start: 16 outliers final: 14 residues processed: 46 average time/residue: 0.2743 time to fit residues: 13.4758 Evaluate side-chains 51 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 37 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 202 CYS Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain B residue 290 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 30 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 42 optimal weight: 0.4980 chunk 5 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 261 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4747 r_free = 0.4747 target = 0.226413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.213051 restraints weight = 5838.452| |-----------------------------------------------------------------------------| r_work (start): 0.4620 rms_B_bonded: 2.18 r_work: 0.4519 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.4519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5614 moved from start: 0.4434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 3985 Z= 0.182 Angle : 0.711 11.804 5403 Z= 0.376 Chirality : 0.045 0.333 617 Planarity : 0.004 0.036 667 Dihedral : 5.030 28.426 555 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.71 % Allowed : 16.83 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.38), residues: 489 helix: 0.94 (0.25), residues: 382 sheet: None (None), residues: 0 loop : -1.24 (0.68), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 87 TYR 0.011 0.001 TYR B 130 PHE 0.013 0.001 PHE B 126 TRP 0.011 0.001 TRP A 95 HIS 0.001 0.000 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 3985) covalent geometry : angle 0.71146 ( 5403) hydrogen bonds : bond 0.04715 ( 308) hydrogen bonds : angle 5.14599 ( 924) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 36 time to evaluate : 0.126 Fit side-chains revert: symmetry clash REVERT: A 224 TYR cc_start: 0.6610 (t80) cc_final: 0.6296 (t80) REVERT: B 26 LEU cc_start: 0.6202 (mt) cc_final: 0.5878 (mt) REVERT: B 90 ASN cc_start: 0.6967 (t0) cc_final: 0.6750 (t0) outliers start: 15 outliers final: 14 residues processed: 44 average time/residue: 0.2817 time to fit residues: 13.2684 Evaluate side-chains 49 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 35 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 202 CYS Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain B residue 290 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 34 optimal weight: 0.0270 chunk 24 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 21 optimal weight: 0.1980 chunk 15 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 chunk 14 optimal weight: 0.0270 chunk 33 optimal weight: 0.2980 chunk 28 optimal weight: 0.7980 overall best weight: 0.2296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 261 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4785 r_free = 0.4785 target = 0.230163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.216975 restraints weight = 5897.265| |-----------------------------------------------------------------------------| r_work (start): 0.4668 rms_B_bonded: 2.18 r_work: 0.4567 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.4567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5511 moved from start: 0.4638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3985 Z= 0.141 Angle : 0.657 10.751 5403 Z= 0.346 Chirality : 0.044 0.328 617 Planarity : 0.004 0.034 667 Dihedral : 4.866 27.419 555 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.91 % Favored : 94.89 % Rotamer: Outliers : 3.96 % Allowed : 16.83 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.38), residues: 489 helix: 1.11 (0.25), residues: 384 sheet: None (None), residues: 0 loop : -1.03 (0.70), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 87 TYR 0.009 0.001 TYR B 130 PHE 0.013 0.001 PHE B 126 TRP 0.011 0.001 TRP A 95 HIS 0.002 0.000 HIS B 250 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 3985) covalent geometry : angle 0.65713 ( 5403) hydrogen bonds : bond 0.04158 ( 308) hydrogen bonds : angle 4.95088 ( 924) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 34 time to evaluate : 0.109 Fit side-chains revert: symmetry clash REVERT: A 224 TYR cc_start: 0.6493 (t80) cc_final: 0.6223 (t80) REVERT: B 26 LEU cc_start: 0.6067 (mt) cc_final: 0.5751 (mt) REVERT: B 90 ASN cc_start: 0.6831 (t0) cc_final: 0.6609 (t0) outliers start: 16 outliers final: 13 residues processed: 43 average time/residue: 0.2901 time to fit residues: 13.3242 Evaluate side-chains 45 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 32 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 202 CYS Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain B residue 290 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 26 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 43 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 32 optimal weight: 0.0870 chunk 22 optimal weight: 0.5980 chunk 24 optimal weight: 0.1980 chunk 4 optimal weight: 0.0050 chunk 45 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.2972 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 261 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4788 r_free = 0.4788 target = 0.230359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.217234 restraints weight = 5812.251| |-----------------------------------------------------------------------------| r_work (start): 0.4670 rms_B_bonded: 2.16 r_work: 0.4567 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.4567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5523 moved from start: 0.4740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3985 Z= 0.145 Angle : 0.696 12.859 5403 Z= 0.361 Chirality : 0.042 0.323 617 Planarity : 0.004 0.034 667 Dihedral : 4.803 26.663 555 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.09 % Favored : 95.71 % Rotamer: Outliers : 3.47 % Allowed : 17.33 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.38), residues: 489 helix: 1.21 (0.25), residues: 385 sheet: None (None), residues: 0 loop : -0.97 (0.70), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 87 TYR 0.010 0.001 TYR B 130 PHE 0.013 0.001 PHE B 126 TRP 0.012 0.001 TRP A 95 HIS 0.001 0.000 HIS A 64 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 3985) covalent geometry : angle 0.69577 ( 5403) hydrogen bonds : bond 0.04167 ( 308) hydrogen bonds : angle 4.94465 ( 924) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1110.00 seconds wall clock time: 19 minutes 40.88 seconds (1180.88 seconds total)