Starting phenix.real_space_refine on Fri Aug 22 15:11:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eke_28200/08_2025/8eke_28200.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eke_28200/08_2025/8eke_28200.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8eke_28200/08_2025/8eke_28200.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eke_28200/08_2025/8eke_28200.map" model { file = "/net/cci-nas-00/data/ceres_data/8eke_28200/08_2025/8eke_28200.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eke_28200/08_2025/8eke_28200.cif" } resolution = 3.36 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= 0.000 sd= 0.014 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 42 5.16 5 C 2966 2.51 5 N 791 2.21 5 O 882 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4681 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2343 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 291} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 2338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2338 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 291} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 14 Time building chain proxies: 1.27, per 1000 atoms: 0.27 Number of scatterers: 4681 At special positions: 0 Unit cell: (89.046, 68.967, 79.443, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 882 8.00 N 791 7.00 C 2966 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: 0.37 Conformation dependent library (CDL) restraints added in 189.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1116 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 6 sheets defined 29.8% alpha, 25.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 13 through 15 No H-bonds generated for 'chain 'A' and resid 13 through 15' Processing helix chain 'A' and resid 41 through 44 Processing helix chain 'A' and resid 46 through 50 removed outlier: 3.619A pdb=" N LEU A 50 " --> pdb=" O GLU A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 61 removed outlier: 3.901A pdb=" N LEU A 57 " --> pdb=" O ASN A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 215 removed outlier: 3.621A pdb=" N VAL A 204 " --> pdb=" O ILE A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 237 removed outlier: 3.886A pdb=" N PHE A 230 " --> pdb=" O THR A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 249 Processing helix chain 'A' and resid 250 through 258 Processing helix chain 'A' and resid 260 through 275 Processing helix chain 'A' and resid 292 through 302 Processing helix chain 'B' and resid 13 through 15 No H-bonds generated for 'chain 'B' and resid 13 through 15' Processing helix chain 'B' and resid 41 through 43 No H-bonds generated for 'chain 'B' and resid 41 through 43' Processing helix chain 'B' and resid 46 through 50 removed outlier: 3.567A pdb=" N LEU B 50 " --> pdb=" O GLU B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 61 removed outlier: 3.792A pdb=" N LEU B 57 " --> pdb=" O ASN B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 215 removed outlier: 4.127A pdb=" N VAL B 204 " --> pdb=" O ILE B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 237 removed outlier: 3.921A pdb=" N PHE B 230 " --> pdb=" O THR B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 249 Processing helix chain 'B' and resid 250 through 258 Processing helix chain 'B' and resid 260 through 275 Processing helix chain 'B' and resid 292 through 302 Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 74 removed outlier: 8.783A pdb=" N ASN A 28 " --> pdb=" O PRO A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 103 removed outlier: 6.492A pdb=" N GLY A 149 " --> pdb=" O CYS A 160 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N VAL A 148 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU A 115 " --> pdb=" O VAL A 148 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N ILE A 152 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 11.412A pdb=" N THR A 111 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N PHE A 112 " --> pdb=" O GLN A 127 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N GLN A 127 " --> pdb=" O PHE A 112 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL A 114 " --> pdb=" O VAL A 125 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL A 125 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA A 116 " --> pdb=" O SER A 123 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 103 removed outlier: 7.041A pdb=" N ALA A 173 " --> pdb=" O HIS A 164 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 73 through 74 removed outlier: 8.786A pdb=" N ASN B 28 " --> pdb=" O PRO B 39 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 101 through 103 removed outlier: 6.471A pdb=" N GLY B 149 " --> pdb=" O CYS B 160 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N VAL B 148 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU B 115 " --> pdb=" O VAL B 148 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N ILE B 152 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 11.426A pdb=" N THR B 111 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N PHE B 112 " --> pdb=" O GLN B 127 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N GLN B 127 " --> pdb=" O PHE B 112 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL B 114 " --> pdb=" O VAL B 125 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N VAL B 125 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ALA B 116 " --> pdb=" O SER B 123 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 101 through 103 183 hydrogen bonds defined for protein. 504 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: 0.52 Time building geometry restraints manager: 0.50 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: 1544 1.34 - 1.46: 1084 1.46 - 1.58: 2095 1.58 - 1.69: 0 1.69 - 1.81: 62 Bond restraints: 4785 Sorted by residual: bond pdb=" C ILE A 78 " pdb=" O ILE A 78 " ideal model delta sigma weight residual 1.241 1.232 0.009 1.06e-02 8.90e+03 7.02e-01 bond pdb=" CB PRO B 99 " pdb=" CG PRO B 99 " ideal model delta sigma weight residual 1.492 1.531 -0.039 5.00e-02 4.00e+02 6.16e-01 bond pdb=" CB PRO A 99 " pdb=" CG PRO A 99 " ideal model delta sigma weight residual 1.492 1.530 -0.038 5.00e-02 4.00e+02 5.86e-01 bond pdb=" CB PRO A 52 " pdb=" CG PRO A 52 " ideal model delta sigma weight residual 1.492 1.523 -0.031 5.00e-02 4.00e+02 3.81e-01 bond pdb=" CA PRO A 184 " pdb=" C PRO A 184 " ideal model delta sigma weight residual 1.527 1.520 0.007 1.07e-02 8.73e+03 3.81e-01 ... (remaining 4780 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.84: 6175 0.84 - 1.69: 268 1.69 - 2.53: 29 2.53 - 3.38: 27 3.38 - 4.22: 10 Bond angle restraints: 6509 Sorted by residual: angle pdb=" N ILE B 43 " pdb=" CA ILE B 43 " pdb=" C ILE B 43 " ideal model delta sigma weight residual 113.07 108.97 4.10 1.36e+00 5.41e-01 9.10e+00 angle pdb=" C GLU A 166 " pdb=" N LEU A 167 " pdb=" CA LEU A 167 " ideal model delta sigma weight residual 121.03 118.16 2.87 1.60e+00 3.91e-01 3.22e+00 angle pdb=" CA PRO A 184 " pdb=" C PRO A 184 " pdb=" O PRO A 184 " ideal model delta sigma weight residual 123.16 120.49 2.67 1.49e+00 4.50e-01 3.21e+00 angle pdb=" N VAL A 247 " pdb=" CA VAL A 247 " pdb=" C VAL A 247 " ideal model delta sigma weight residual 113.16 110.58 2.58 1.49e+00 4.50e-01 2.99e+00 angle pdb=" N VAL B 247 " pdb=" CA VAL B 247 " pdb=" C VAL B 247 " ideal model delta sigma weight residual 113.16 110.71 2.45 1.49e+00 4.50e-01 2.71e+00 ... (remaining 6504 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.75: 2615 13.75 - 27.50: 135 27.50 - 41.26: 40 41.26 - 55.01: 16 55.01 - 68.76: 5 Dihedral angle restraints: 2811 sinusoidal: 1065 harmonic: 1746 Sorted by residual: dihedral pdb=" CA ASN B 53 " pdb=" C ASN B 53 " pdb=" N TYR B 54 " pdb=" CA TYR B 54 " ideal model delta harmonic sigma weight residual 180.00 -162.91 -17.09 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA MET A 264 " pdb=" CB MET A 264 " pdb=" CG MET A 264 " pdb=" SD MET A 264 " ideal model delta sinusoidal sigma weight residual 60.00 119.11 -59.11 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA ARG A 60 " pdb=" CB ARG A 60 " pdb=" CG ARG A 60 " pdb=" CD ARG A 60 " ideal model delta sinusoidal sigma weight residual 180.00 127.49 52.51 3 1.50e+01 4.44e-03 9.12e+00 ... (remaining 2808 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 405 0.023 - 0.046: 184 0.046 - 0.070: 88 0.070 - 0.093: 34 0.093 - 0.116: 29 Chirality restraints: 740 Sorted by residual: chirality pdb=" CA VAL A 35 " pdb=" N VAL A 35 " pdb=" C VAL A 35 " pdb=" CB VAL A 35 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.36e-01 chirality pdb=" CA VAL B 35 " pdb=" N VAL B 35 " pdb=" C VAL B 35 " pdb=" CB VAL B 35 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.14e-01 chirality pdb=" CA ILE A 281 " pdb=" N ILE A 281 " pdb=" C ILE A 281 " pdb=" CB ILE A 281 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.14e-01 ... (remaining 737 not shown) Planarity restraints: 848 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 251 " -0.024 5.00e-02 4.00e+02 3.64e-02 2.12e+00 pdb=" N PRO B 252 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO B 252 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 252 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 251 " 0.024 5.00e-02 4.00e+02 3.61e-02 2.09e+00 pdb=" N PRO A 252 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 252 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 252 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B 38 " -0.018 5.00e-02 4.00e+02 2.74e-02 1.20e+00 pdb=" N PRO B 39 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO B 39 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 39 " -0.015 5.00e-02 4.00e+02 ... (remaining 845 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1520 2.83 - 3.35: 4130 3.35 - 3.87: 7287 3.87 - 4.38: 8302 4.38 - 4.90: 14609 Nonbonded interactions: 35848 Sorted by model distance: nonbonded pdb=" OG SER A 254 " pdb=" O ILE A 259 " model vdw 2.313 3.040 nonbonded pdb=" OH TYR B 209 " pdb=" O ILE B 259 " model vdw 2.341 3.040 nonbonded pdb=" N ASN B 28 " pdb=" OD1 ASN B 28 " model vdw 2.343 3.120 nonbonded pdb=" OD1 ASN A 133 " pdb=" OG1 THR A 135 " model vdw 2.381 3.040 nonbonded pdb=" N ASP B 263 " pdb=" OD1 ASP B 263 " model vdw 2.384 3.120 ... (remaining 35843 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 1 through 206 or (resid 207 and (name N or name CA or name \ C or name O or name CB )) or resid 208 through 305)) selection = (chain 'B' and (resid 1 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB )) or resid 15 through 305)) } 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: 2.000 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.420 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.000 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 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 0.039 4785 Z= 0.089 Angle : 0.447 4.222 6509 Z= 0.245 Chirality : 0.038 0.116 740 Planarity : 0.003 0.036 848 Dihedral : 10.502 68.761 1695 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.33 % Allowed : 2.48 % Favored : 97.19 % Rotamer: Outliers : 2.71 % Allowed : 8.53 % Favored : 88.76 % 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 aren not related in a simple way. whole: -0.29 (0.34), residues: 606 helix: 0.58 (0.44), residues: 162 sheet: -0.49 (0.48), residues: 106 loop : -0.40 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 222 TYR 0.006 0.001 TYR A 239 PHE 0.005 0.001 PHE A 230 TRP 0.006 0.001 TRP A 207 HIS 0.002 0.000 HIS B 64 Details of bonding type rmsd covalent geometry : bond 0.00181 ( 4785) covalent geometry : angle 0.44705 ( 6509) hydrogen bonds : bond 0.21513 ( 179) hydrogen bonds : angle 7.69628 ( 504) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 145 time to evaluate : 0.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LYS cc_start: 0.7014 (ptpt) cc_final: 0.6792 (ptpt) REVERT: A 222 ARG cc_start: 0.5648 (mmm-85) cc_final: 0.5407 (mmm-85) REVERT: B 49 MET cc_start: 0.4720 (tpp) cc_final: 0.4485 (tpp) REVERT: B 93 THR cc_start: 0.8797 (m) cc_final: 0.8574 (p) REVERT: B 222 ARG cc_start: 0.5722 (mmm-85) cc_final: 0.5442 (mmm-85) REVERT: B 238 ASN cc_start: 0.7391 (t0) cc_final: 0.7183 (t0) outliers start: 14 outliers final: 5 residues processed: 156 average time/residue: 0.0713 time to fit residues: 13.7614 Evaluate side-chains 105 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 100 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 263 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.0670 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 58 optimal weight: 0.0270 overall best weight: 0.4976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN ** A 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 299 GLN B 84 ASN B 110 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.165158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.152801 restraints weight = 9879.095| |-----------------------------------------------------------------------------| r_work (start): 0.4125 rms_B_bonded: 3.54 r_work: 0.4008 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.4008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4785 Z= 0.117 Angle : 0.564 6.935 6509 Z= 0.289 Chirality : 0.041 0.149 740 Planarity : 0.004 0.035 848 Dihedral : 4.510 42.311 659 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.13 % Favored : 95.54 % Rotamer: Outliers : 5.23 % Allowed : 14.92 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.34), residues: 606 helix: 0.76 (0.44), residues: 164 sheet: -1.00 (0.47), residues: 90 loop : -0.40 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 4 TYR 0.014 0.001 TYR A 239 PHE 0.014 0.001 PHE A 230 TRP 0.007 0.001 TRP A 207 HIS 0.004 0.001 HIS A 172 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 4785) covalent geometry : angle 0.56395 ( 6509) hydrogen bonds : bond 0.03820 ( 179) hydrogen bonds : angle 5.76038 ( 504) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 124 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 MET cc_start: 0.8999 (tpp) cc_final: 0.8545 (ttm) REVERT: A 77 VAL cc_start: 0.5005 (OUTLIER) cc_final: 0.4705 (m) REVERT: A 102 LYS cc_start: 0.8529 (mmmm) cc_final: 0.8312 (mmmt) REVERT: A 152 ILE cc_start: 0.8674 (tp) cc_final: 0.8386 (mt) REVERT: A 207 TRP cc_start: 0.8968 (t60) cc_final: 0.8136 (t60) REVERT: A 222 ARG cc_start: 0.6038 (mmm-85) cc_final: 0.5749 (mmm-85) REVERT: B 28 ASN cc_start: 0.8048 (OUTLIER) cc_final: 0.7814 (p0) REVERT: B 49 MET cc_start: 0.5066 (tpp) cc_final: 0.4802 (tpp) REVERT: B 152 ILE cc_start: 0.8701 (tp) cc_final: 0.8455 (mt) REVERT: B 222 ARG cc_start: 0.5956 (mmm-85) cc_final: 0.5639 (mmm-85) REVERT: B 238 ASN cc_start: 0.7504 (t0) cc_final: 0.7301 (t0) outliers start: 27 outliers final: 13 residues processed: 138 average time/residue: 0.0803 time to fit residues: 13.6430 Evaluate side-chains 132 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 53 ASN Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 235 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 51 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 10 optimal weight: 0.0050 chunk 52 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN A 192 GLN A 299 GLN B 84 ASN B 110 GLN B 192 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.163784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.151401 restraints weight = 9917.113| |-----------------------------------------------------------------------------| r_work (start): 0.4108 rms_B_bonded: 3.44 r_work: 0.3997 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4785 Z= 0.131 Angle : 0.548 5.551 6509 Z= 0.284 Chirality : 0.041 0.136 740 Planarity : 0.004 0.037 848 Dihedral : 4.728 44.223 655 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.29 % Favored : 95.38 % Rotamer: Outliers : 6.20 % Allowed : 16.47 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.34), residues: 606 helix: 0.63 (0.43), residues: 166 sheet: -1.07 (0.46), residues: 90 loop : -0.54 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 4 TYR 0.018 0.001 TYR A 239 PHE 0.017 0.001 PHE A 230 TRP 0.005 0.001 TRP A 207 HIS 0.005 0.001 HIS A 172 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 4785) covalent geometry : angle 0.54822 ( 6509) hydrogen bonds : bond 0.03573 ( 179) hydrogen bonds : angle 5.29921 ( 504) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 0.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 VAL cc_start: 0.5287 (OUTLIER) cc_final: 0.4920 (m) REVERT: A 152 ILE cc_start: 0.8699 (tp) cc_final: 0.8422 (mt) REVERT: A 222 ARG cc_start: 0.6037 (mmm-85) cc_final: 0.5751 (mmm-85) REVERT: A 247 VAL cc_start: 0.4397 (OUTLIER) cc_final: 0.4177 (p) REVERT: B 17 MET cc_start: 0.8784 (tpp) cc_final: 0.8418 (ttp) REVERT: B 28 ASN cc_start: 0.8211 (OUTLIER) cc_final: 0.7957 (p0) REVERT: B 49 MET cc_start: 0.5117 (tpp) cc_final: 0.4822 (tpp) REVERT: B 110 GLN cc_start: 0.8314 (mt0) cc_final: 0.8055 (mt0) REVERT: B 152 ILE cc_start: 0.8751 (tp) cc_final: 0.8404 (mt) REVERT: B 222 ARG cc_start: 0.5951 (mmm-85) cc_final: 0.5638 (mmm-85) outliers start: 32 outliers final: 21 residues processed: 144 average time/residue: 0.0742 time to fit residues: 13.2292 Evaluate side-chains 151 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 53 ASN Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 280 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 53 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 57 optimal weight: 0.3980 chunk 38 optimal weight: 2.9990 chunk 55 optimal weight: 0.0270 chunk 59 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN A 110 GLN B 84 ASN B 192 GLN B 299 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.163942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.151292 restraints weight = 9793.437| |-----------------------------------------------------------------------------| r_work (start): 0.4100 rms_B_bonded: 3.45 r_work: 0.3989 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4785 Z= 0.124 Angle : 0.550 6.136 6509 Z= 0.283 Chirality : 0.041 0.160 740 Planarity : 0.004 0.038 848 Dihedral : 4.740 44.387 655 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.96 % Favored : 95.71 % Rotamer: Outliers : 6.59 % Allowed : 18.02 % Favored : 75.39 % 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 aren not related in a simple way. whole: -0.61 (0.34), residues: 606 helix: 0.66 (0.43), residues: 166 sheet: -1.09 (0.44), residues: 110 loop : -0.65 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 4 TYR 0.010 0.001 TYR B 239 PHE 0.014 0.001 PHE A 230 TRP 0.006 0.001 TRP A 207 HIS 0.003 0.001 HIS B 172 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 4785) covalent geometry : angle 0.55025 ( 6509) hydrogen bonds : bond 0.03232 ( 179) hydrogen bonds : angle 5.06789 ( 504) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 129 time to evaluate : 0.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 PHE cc_start: 0.9118 (m-10) cc_final: 0.8897 (m-10) REVERT: A 77 VAL cc_start: 0.5329 (OUTLIER) cc_final: 0.4960 (m) REVERT: A 119 ASN cc_start: 0.8540 (t0) cc_final: 0.8245 (t0) REVERT: A 152 ILE cc_start: 0.8655 (tp) cc_final: 0.8395 (mt) REVERT: A 222 ARG cc_start: 0.5977 (mmm-85) cc_final: 0.5679 (mmm-85) REVERT: A 247 VAL cc_start: 0.4400 (OUTLIER) cc_final: 0.4173 (p) REVERT: B 17 MET cc_start: 0.8738 (tpp) cc_final: 0.8515 (ttp) REVERT: B 28 ASN cc_start: 0.8255 (OUTLIER) cc_final: 0.8038 (p0) REVERT: B 49 MET cc_start: 0.5144 (tpp) cc_final: 0.4829 (tpp) REVERT: B 152 ILE cc_start: 0.8660 (tp) cc_final: 0.8351 (mt) REVERT: B 222 ARG cc_start: 0.6054 (mmm-85) cc_final: 0.5768 (mmm-85) outliers start: 34 outliers final: 23 residues processed: 147 average time/residue: 0.0695 time to fit residues: 12.6810 Evaluate side-chains 149 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 123 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 53 ASN Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 88 LYS Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 287 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 49 optimal weight: 0.0050 chunk 28 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 47 optimal weight: 0.1980 chunk 16 optimal weight: 0.0470 chunk 55 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 overall best weight: 0.2892 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN A 192 GLN B 84 ASN B 110 GLN B 192 GLN B 299 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.165909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.153564 restraints weight = 9875.049| |-----------------------------------------------------------------------------| r_work (start): 0.4130 rms_B_bonded: 3.46 r_work: 0.4020 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.4020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 4785 Z= 0.099 Angle : 0.561 7.270 6509 Z= 0.281 Chirality : 0.041 0.131 740 Planarity : 0.004 0.039 848 Dihedral : 4.568 44.229 655 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.80 % Favored : 96.04 % Rotamer: Outliers : 4.84 % Allowed : 19.38 % Favored : 75.78 % 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 aren not related in a simple way. whole: -0.21 (0.34), residues: 606 helix: 1.24 (0.44), residues: 154 sheet: -0.64 (0.43), residues: 120 loop : -0.55 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 4 TYR 0.011 0.001 TYR A 101 PHE 0.010 0.001 PHE B 181 TRP 0.004 0.001 TRP A 31 HIS 0.003 0.001 HIS A 172 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 4785) covalent geometry : angle 0.56077 ( 6509) hydrogen bonds : bond 0.02758 ( 179) hydrogen bonds : angle 4.86852 ( 504) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 0.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 VAL cc_start: 0.5319 (OUTLIER) cc_final: 0.4945 (m) REVERT: A 119 ASN cc_start: 0.8456 (t0) cc_final: 0.8232 (t0) REVERT: A 152 ILE cc_start: 0.8530 (tp) cc_final: 0.8271 (mt) REVERT: A 222 ARG cc_start: 0.5930 (mmm-85) cc_final: 0.5676 (mmm-85) REVERT: A 247 VAL cc_start: 0.4312 (OUTLIER) cc_final: 0.4085 (p) REVERT: B 49 MET cc_start: 0.5082 (tpp) cc_final: 0.4646 (tpt) REVERT: B 83 GLN cc_start: 0.7261 (pp30) cc_final: 0.7008 (pp30) REVERT: B 152 ILE cc_start: 0.8651 (tp) cc_final: 0.8360 (mt) REVERT: B 222 ARG cc_start: 0.5998 (mmm-85) cc_final: 0.5722 (mmm-85) outliers start: 25 outliers final: 18 residues processed: 144 average time/residue: 0.0764 time to fit residues: 13.6303 Evaluate side-chains 146 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 287 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 10 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 4 optimal weight: 0.3980 chunk 51 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 30 optimal weight: 0.0040 chunk 9 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN A 192 GLN B 28 ASN B 84 ASN B 110 GLN B 180 ASN B 192 GLN B 299 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.163630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.150726 restraints weight = 9845.894| |-----------------------------------------------------------------------------| r_work (start): 0.4103 rms_B_bonded: 3.59 r_work: 0.3988 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4785 Z= 0.128 Angle : 0.583 5.752 6509 Z= 0.295 Chirality : 0.042 0.143 740 Planarity : 0.004 0.037 848 Dihedral : 4.642 45.029 653 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.96 % Favored : 95.87 % Rotamer: Outliers : 5.62 % Allowed : 19.19 % Favored : 75.19 % 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 aren not related in a simple way. whole: -0.56 (0.34), residues: 606 helix: 0.71 (0.43), residues: 166 sheet: -1.35 (0.52), residues: 84 loop : -0.60 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 4 TYR 0.013 0.001 TYR A 239 PHE 0.014 0.001 PHE A 230 TRP 0.005 0.001 TRP A 207 HIS 0.003 0.001 HIS A 172 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 4785) covalent geometry : angle 0.58277 ( 6509) hydrogen bonds : bond 0.03190 ( 179) hydrogen bonds : angle 4.91621 ( 504) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 0.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 MET cc_start: 0.8929 (ttm) cc_final: 0.8619 (ttp) REVERT: A 77 VAL cc_start: 0.5360 (OUTLIER) cc_final: 0.5126 (t) REVERT: A 119 ASN cc_start: 0.8502 (t0) cc_final: 0.8211 (t0) REVERT: A 222 ARG cc_start: 0.6106 (mmm-85) cc_final: 0.5854 (mmm-85) REVERT: A 247 VAL cc_start: 0.4386 (OUTLIER) cc_final: 0.4166 (p) REVERT: B 49 MET cc_start: 0.5131 (tpp) cc_final: 0.4696 (tpt) REVERT: B 222 ARG cc_start: 0.6157 (mmm-85) cc_final: 0.5854 (mmm-85) outliers start: 29 outliers final: 25 residues processed: 148 average time/residue: 0.0759 time to fit residues: 13.8792 Evaluate side-chains 149 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 53 ASN Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 287 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 29 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 59 optimal weight: 0.0980 chunk 53 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN A 192 GLN B 84 ASN B 110 GLN B 192 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.162936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.150092 restraints weight = 9752.937| |-----------------------------------------------------------------------------| r_work (start): 0.4095 rms_B_bonded: 3.50 r_work: 0.3983 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4785 Z= 0.143 Angle : 0.619 6.108 6509 Z= 0.319 Chirality : 0.042 0.143 740 Planarity : 0.004 0.037 848 Dihedral : 4.309 23.527 651 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 5.62 % Allowed : 19.57 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.33), residues: 606 helix: 0.54 (0.42), residues: 166 sheet: -1.33 (0.51), residues: 84 loop : -0.64 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 4 TYR 0.008 0.001 TYR B 101 PHE 0.016 0.001 PHE A 230 TRP 0.004 0.001 TRP A 31 HIS 0.003 0.001 HIS A 172 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 4785) covalent geometry : angle 0.61899 ( 6509) hydrogen bonds : bond 0.03297 ( 179) hydrogen bonds : angle 4.97508 ( 504) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 128 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 VAL cc_start: 0.5384 (OUTLIER) cc_final: 0.5115 (t) REVERT: A 119 ASN cc_start: 0.8490 (t0) cc_final: 0.8210 (t0) REVERT: A 222 ARG cc_start: 0.6113 (mmm-85) cc_final: 0.5828 (mmm-85) REVERT: A 247 VAL cc_start: 0.4463 (OUTLIER) cc_final: 0.4257 (p) REVERT: A 259 ILE cc_start: 0.8602 (mm) cc_final: 0.8402 (mm) REVERT: B 49 MET cc_start: 0.5145 (tpp) cc_final: 0.4752 (tpt) REVERT: B 85 CYS cc_start: 0.8861 (t) cc_final: 0.8427 (t) REVERT: B 90 LYS cc_start: 0.8187 (ttmm) cc_final: 0.7893 (ttpp) REVERT: B 222 ARG cc_start: 0.6158 (mmm-85) cc_final: 0.5856 (mmm-85) outliers start: 29 outliers final: 21 residues processed: 146 average time/residue: 0.0794 time to fit residues: 14.2297 Evaluate side-chains 147 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 53 ASN Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 287 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 44 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 38 optimal weight: 0.4980 chunk 19 optimal weight: 6.9990 chunk 43 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN B 84 ASN B 110 GLN B 192 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.162890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.149640 restraints weight = 9887.331| |-----------------------------------------------------------------------------| r_work (start): 0.4081 rms_B_bonded: 3.53 r_work: 0.3962 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4785 Z= 0.148 Angle : 0.640 6.450 6509 Z= 0.327 Chirality : 0.043 0.147 740 Planarity : 0.004 0.039 848 Dihedral : 4.442 26.900 651 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 5.04 % Allowed : 19.96 % Favored : 75.00 % 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 aren not related in a simple way. whole: -0.73 (0.33), residues: 606 helix: 0.46 (0.42), residues: 166 sheet: -1.41 (0.51), residues: 84 loop : -0.67 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 4 TYR 0.008 0.001 TYR B 239 PHE 0.017 0.001 PHE A 230 TRP 0.005 0.001 TRP B 31 HIS 0.003 0.001 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 4785) covalent geometry : angle 0.64014 ( 6509) hydrogen bonds : bond 0.03377 ( 179) hydrogen bonds : angle 5.03324 ( 504) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 VAL cc_start: 0.5414 (OUTLIER) cc_final: 0.5167 (t) REVERT: A 119 ASN cc_start: 0.8478 (t0) cc_final: 0.8247 (t0) REVERT: A 166 GLU cc_start: 0.8662 (tp30) cc_final: 0.8345 (tp30) REVERT: A 222 ARG cc_start: 0.6170 (mmm-85) cc_final: 0.5915 (mmm-85) REVERT: A 247 VAL cc_start: 0.4622 (OUTLIER) cc_final: 0.4413 (p) REVERT: B 49 MET cc_start: 0.5090 (tpp) cc_final: 0.4718 (tpt) REVERT: B 90 LYS cc_start: 0.8206 (ttmm) cc_final: 0.7891 (ttpp) REVERT: B 222 ARG cc_start: 0.6243 (mmm-85) cc_final: 0.5969 (mmm-85) outliers start: 26 outliers final: 21 residues processed: 140 average time/residue: 0.0903 time to fit residues: 15.5977 Evaluate side-chains 145 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 53 ASN Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 117 CYS Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 287 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 59 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 3 optimal weight: 0.0470 chunk 8 optimal weight: 0.3980 chunk 41 optimal weight: 0.0370 chunk 24 optimal weight: 0.0270 chunk 28 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.2214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN A 192 GLN B 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.166072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.153294 restraints weight = 9629.180| |-----------------------------------------------------------------------------| r_work (start): 0.4125 rms_B_bonded: 3.48 r_work: 0.4015 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.4015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4785 Z= 0.110 Angle : 0.629 6.650 6509 Z= 0.314 Chirality : 0.041 0.129 740 Planarity : 0.004 0.042 848 Dihedral : 4.167 26.677 651 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 4.07 % Allowed : 20.54 % Favored : 75.39 % 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 aren not related in a simple way. whole: -0.57 (0.34), residues: 606 helix: 0.64 (0.42), residues: 166 sheet: -1.49 (0.50), residues: 84 loop : -0.52 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 76 TYR 0.011 0.001 TYR A 239 PHE 0.006 0.001 PHE B 181 TRP 0.005 0.001 TRP B 31 HIS 0.002 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 4785) covalent geometry : angle 0.62891 ( 6509) hydrogen bonds : bond 0.02768 ( 179) hydrogen bonds : angle 4.92990 ( 504) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASN cc_start: 0.8441 (t0) cc_final: 0.8139 (t0) REVERT: A 166 GLU cc_start: 0.8586 (tp30) cc_final: 0.8234 (tp30) REVERT: A 222 ARG cc_start: 0.6175 (mmm-85) cc_final: 0.5939 (mmm-85) REVERT: A 247 VAL cc_start: 0.4413 (OUTLIER) cc_final: 0.4194 (p) REVERT: B 49 MET cc_start: 0.5004 (tpp) cc_final: 0.4603 (tpt) REVERT: B 222 ARG cc_start: 0.6183 (mmm-85) cc_final: 0.5922 (mmm-85) outliers start: 21 outliers final: 16 residues processed: 141 average time/residue: 0.0746 time to fit residues: 12.8263 Evaluate side-chains 142 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 117 CYS Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 287 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 0.7980 chunk 16 optimal weight: 0.0030 chunk 25 optimal weight: 0.0170 chunk 22 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 33 optimal weight: 0.0770 chunk 8 optimal weight: 2.9990 overall best weight: 0.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 ASN B 164 HIS B 192 GLN B 299 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.165625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.152612 restraints weight = 9825.373| |-----------------------------------------------------------------------------| r_work (start): 0.4114 rms_B_bonded: 3.52 r_work: 0.4001 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.4001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4785 Z= 0.117 Angle : 0.659 9.493 6509 Z= 0.327 Chirality : 0.042 0.134 740 Planarity : 0.004 0.040 848 Dihedral : 4.187 26.617 651 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.29 % Allowed : 21.71 % Favored : 75.00 % 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 aren not related in a simple way. whole: -0.54 (0.34), residues: 606 helix: 0.66 (0.42), residues: 166 sheet: -1.50 (0.51), residues: 84 loop : -0.50 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 4 TYR 0.013 0.001 TYR A 161 PHE 0.008 0.001 PHE B 181 TRP 0.004 0.001 TRP B 31 HIS 0.003 0.001 HIS B 164 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 4785) covalent geometry : angle 0.65874 ( 6509) hydrogen bonds : bond 0.02944 ( 179) hydrogen bonds : angle 4.94479 ( 504) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASN cc_start: 0.8420 (t0) cc_final: 0.8130 (t0) REVERT: A 222 ARG cc_start: 0.6209 (mmm-85) cc_final: 0.5983 (mmm-85) REVERT: B 49 MET cc_start: 0.4966 (tpp) cc_final: 0.4577 (tpt) REVERT: B 222 ARG cc_start: 0.6175 (mmm-85) cc_final: 0.5910 (mmm-85) outliers start: 17 outliers final: 13 residues processed: 135 average time/residue: 0.0746 time to fit residues: 12.3588 Evaluate side-chains 136 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 287 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 27 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 10 optimal weight: 0.4980 chunk 43 optimal weight: 0.0170 chunk 38 optimal weight: 2.9990 chunk 59 optimal weight: 0.0770 chunk 12 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN A 192 GLN B 84 ASN B 164 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.164970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.151818 restraints weight = 9813.451| |-----------------------------------------------------------------------------| r_work (start): 0.4103 rms_B_bonded: 3.55 r_work: 0.3991 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4785 Z= 0.125 Angle : 0.672 9.426 6509 Z= 0.337 Chirality : 0.042 0.137 740 Planarity : 0.004 0.040 848 Dihedral : 4.214 26.786 651 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.71 % Allowed : 22.29 % Favored : 75.00 % 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 aren not related in a simple way. whole: -0.53 (0.34), residues: 606 helix: 0.68 (0.42), residues: 166 sheet: -1.41 (0.51), residues: 84 loop : -0.52 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 4 TYR 0.014 0.001 TYR A 239 PHE 0.010 0.001 PHE A 230 TRP 0.005 0.001 TRP B 31 HIS 0.003 0.001 HIS B 164 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 4785) covalent geometry : angle 0.67157 ( 6509) hydrogen bonds : bond 0.02969 ( 179) hydrogen bonds : angle 4.89640 ( 504) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1163.30 seconds wall clock time: 20 minutes 37.39 seconds (1237.39 seconds total)