Starting phenix.real_space_refine on Thu Mar 6 03:37:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eke_28200/03_2025/8eke_28200.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eke_28200/03_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_28200/03_2025/8eke_28200.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eke_28200/03_2025/8eke_28200.map" model { file = "/net/cci-nas-00/data/ceres_data/8eke_28200/03_2025/8eke_28200.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eke_28200/03_2025/8eke_28200.cif" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 3.86, per 1000 atoms: 0.82 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: 1.17 Conformation dependent library (CDL) restraints added in 544.3 milliseconds 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: 0.60 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: 1.19 Time building geometry restraints manager: 1.38 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: 2.300 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.820 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.480 ------------------------------------------------------------------------------- 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= 0.117 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (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 TRP 0.006 0.001 TRP A 207 HIS 0.002 0.000 HIS B 64 PHE 0.005 0.001 PHE A 230 TYR 0.006 0.001 TYR A 239 ARG 0.001 0.000 ARG A 222 *********************** 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 : 0.564 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: 0.4484 (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: 0.1895 time to fit residues: 36.2865 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 : 0.484 ------------------------------------------------------------------------------- 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 50 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 24 optimal weight: 0.3980 chunk 47 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 54 optimal weight: 0.0000 overall best weight: 1.0790 ------------------------------------------------------------------------------- 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 28 ASN B 84 ASN B 110 GLN B 180 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.161325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.148314 restraints weight = 9747.268| |-----------------------------------------------------------------------------| r_work (start): 0.4068 rms_B_bonded: 3.54 r_work: 0.3948 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4785 Z= 0.276 Angle : 0.623 7.154 6509 Z= 0.327 Chirality : 0.044 0.176 740 Planarity : 0.004 0.034 848 Dihedral : 5.034 45.071 659 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.79 % Favored : 94.88 % Rotamer: Outliers : 6.40 % Allowed : 15.70 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.34), residues: 606 helix: 0.44 (0.43), residues: 164 sheet: -1.10 (0.50), residues: 82 loop : -0.63 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 207 HIS 0.003 0.001 HIS B 172 PHE 0.026 0.001 PHE A 230 TYR 0.020 0.002 TYR A 239 ARG 0.002 0.000 ARG B 279 *********************** 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 160 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 127 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 MET cc_start: 0.8965 (tpp) cc_final: 0.8689 (ttm) REVERT: A 77 VAL cc_start: 0.5316 (OUTLIER) cc_final: 0.4964 (m) REVERT: A 102 LYS cc_start: 0.8546 (mmmm) cc_final: 0.8340 (mmmt) REVERT: A 207 TRP cc_start: 0.9010 (t60) cc_final: 0.8260 (t60) REVERT: A 222 ARG cc_start: 0.6206 (mmm-85) cc_final: 0.5907 (mmm-85) REVERT: A 247 VAL cc_start: 0.4554 (OUTLIER) cc_final: 0.4338 (p) REVERT: B 28 ASN cc_start: 0.8102 (OUTLIER) cc_final: 0.7885 (p0) REVERT: B 49 MET cc_start: 0.5209 (tpp) cc_final: 0.4980 (tpt) REVERT: B 91 VAL cc_start: 0.4644 (OUTLIER) cc_final: 0.4427 (p) REVERT: B 93 THR cc_start: 0.8684 (m) cc_final: 0.8419 (p) REVERT: B 110 GLN cc_start: 0.8337 (mt0) cc_final: 0.8086 (mt0) REVERT: B 152 ILE cc_start: 0.8700 (tp) cc_final: 0.8463 (mt) REVERT: B 222 ARG cc_start: 0.6173 (mmm-85) cc_final: 0.5858 (mmm-85) REVERT: B 238 ASN cc_start: 0.7577 (t0) cc_final: 0.7311 (t0) outliers start: 33 outliers final: 16 residues processed: 145 average time/residue: 0.1895 time to fit residues: 33.8920 Evaluate side-chains 140 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.537 ------------------------------------------------------------------------------- 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 225 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain B residue 28 ASN 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 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 53 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 37 optimal weight: 0.3980 chunk 50 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 A 192 GLN A 299 GLN B 180 ASN B 192 GLN B 203 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.161852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.149403 restraints weight = 9792.021| |-----------------------------------------------------------------------------| r_work (start): 0.4080 rms_B_bonded: 3.39 r_work: 0.3971 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4785 Z= 0.223 Angle : 0.593 10.912 6509 Z= 0.303 Chirality : 0.042 0.138 740 Planarity : 0.004 0.051 848 Dihedral : 4.968 45.437 655 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.96 % Favored : 95.71 % Rotamer: Outliers : 5.81 % Allowed : 18.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.33), residues: 606 helix: 0.39 (0.42), residues: 166 sheet: -1.19 (0.49), residues: 82 loop : -0.73 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 207 HIS 0.004 0.001 HIS A 172 PHE 0.016 0.001 PHE A 230 TYR 0.019 0.001 TYR A 239 ARG 0.002 0.000 ARG B 279 *********************** 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 153 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 123 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 VAL cc_start: 0.5257 (OUTLIER) cc_final: 0.4882 (m) REVERT: A 152 ILE cc_start: 0.8661 (tp) cc_final: 0.8379 (mt) REVERT: A 222 ARG cc_start: 0.6093 (mmm-85) cc_final: 0.5797 (mmm-85) REVERT: A 247 VAL cc_start: 0.4408 (OUTLIER) cc_final: 0.4197 (p) REVERT: B 17 MET cc_start: 0.8787 (tpp) cc_final: 0.8456 (ttp) REVERT: B 49 MET cc_start: 0.5294 (tpp) cc_final: 0.4949 (tpt) REVERT: B 91 VAL cc_start: 0.4535 (OUTLIER) cc_final: 0.4265 (p) REVERT: B 93 THR cc_start: 0.8691 (m) cc_final: 0.8403 (p) REVERT: B 102 LYS cc_start: 0.8467 (mmmm) cc_final: 0.8190 (mmmt) REVERT: B 152 ILE cc_start: 0.8719 (tp) cc_final: 0.8413 (mt) REVERT: B 222 ARG cc_start: 0.6069 (mmm-85) cc_final: 0.5736 (mmm-85) outliers start: 30 outliers final: 18 residues processed: 142 average time/residue: 0.1851 time to fit residues: 32.3196 Evaluate side-chains 143 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.492 ------------------------------------------------------------------------------- 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 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 32 LEU 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 196 THR Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 287 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 34 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 110 GLN B 180 ASN B 192 GLN B 299 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.161570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.148799 restraints weight = 9685.950| |-----------------------------------------------------------------------------| r_work (start): 0.4070 rms_B_bonded: 3.43 r_work: 0.3959 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.2865 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= 0.230 Angle : 0.593 9.114 6509 Z= 0.303 Chirality : 0.043 0.168 740 Planarity : 0.004 0.052 848 Dihedral : 4.947 45.843 653 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.95 % Favored : 94.72 % Rotamer: Outliers : 5.43 % Allowed : 20.16 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.33), residues: 606 helix: 0.31 (0.42), residues: 166 sheet: -1.18 (0.47), residues: 100 loop : -0.92 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 207 HIS 0.003 0.001 HIS A 172 PHE 0.017 0.001 PHE A 230 TYR 0.015 0.002 TYR A 239 ARG 0.002 0.000 ARG B 4 *********************** 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 154 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 VAL cc_start: 0.5330 (OUTLIER) cc_final: 0.4930 (m) REVERT: A 119 ASN cc_start: 0.8495 (t0) cc_final: 0.8240 (t0) REVERT: A 152 ILE cc_start: 0.8645 (tp) cc_final: 0.8367 (mt) REVERT: A 222 ARG cc_start: 0.6143 (mmm-85) cc_final: 0.5876 (mmm-85) REVERT: A 247 VAL cc_start: 0.4543 (OUTLIER) cc_final: 0.4324 (p) REVERT: B 17 MET cc_start: 0.8729 (tpp) cc_final: 0.8516 (ttp) REVERT: B 49 MET cc_start: 0.5526 (tpp) cc_final: 0.5140 (tpt) REVERT: B 91 VAL cc_start: 0.4534 (OUTLIER) cc_final: 0.4275 (p) REVERT: B 93 THR cc_start: 0.8689 (m) cc_final: 0.8393 (p) REVERT: B 110 GLN cc_start: 0.8316 (mt0) cc_final: 0.8065 (mt0) REVERT: B 152 ILE cc_start: 0.8694 (tp) cc_final: 0.8376 (mt) REVERT: B 199 THR cc_start: 0.8376 (p) cc_final: 0.8142 (p) REVERT: B 200 ILE cc_start: 0.8600 (mt) cc_final: 0.8383 (mm) REVERT: B 222 ARG cc_start: 0.5993 (mmm-85) cc_final: 0.5687 (mmm-85) outliers start: 28 outliers final: 21 residues processed: 142 average time/residue: 0.1946 time to fit residues: 33.9111 Evaluate side-chains 147 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 0.480 ------------------------------------------------------------------------------- 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 9 optimal weight: 0.2980 chunk 23 optimal weight: 0.9990 chunk 30 optimal weight: 0.4980 chunk 13 optimal weight: 0.7980 chunk 31 optimal weight: 0.2980 chunk 34 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 A 192 GLN B 84 ASN 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 = 0.4258 r_free = 0.4258 target = 0.163068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.150128 restraints weight = 9664.581| |-----------------------------------------------------------------------------| r_work (start): 0.4091 rms_B_bonded: 3.52 r_work: 0.3978 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4785 Z= 0.188 Angle : 0.577 7.758 6509 Z= 0.294 Chirality : 0.042 0.142 740 Planarity : 0.004 0.054 848 Dihedral : 4.751 45.230 653 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.96 % Favored : 95.71 % Rotamer: Outliers : 5.23 % Allowed : 19.96 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.33), residues: 606 helix: 0.93 (0.44), residues: 154 sheet: -1.59 (0.49), residues: 88 loop : -0.70 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 31 HIS 0.003 0.001 HIS B 41 PHE 0.011 0.001 PHE A 230 TYR 0.012 0.001 TYR A 101 ARG 0.001 0.000 ARG A 4 *********************** 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 153 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 126 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 VAL cc_start: 0.5311 (OUTLIER) cc_final: 0.4928 (m) REVERT: A 119 ASN cc_start: 0.8529 (t0) cc_final: 0.8263 (t0) REVERT: A 152 ILE cc_start: 0.8593 (tp) cc_final: 0.8318 (mt) REVERT: A 222 ARG cc_start: 0.6116 (mmm-85) cc_final: 0.5858 (mmm-85) REVERT: B 49 MET cc_start: 0.5315 (tpp) cc_final: 0.4942 (tpt) REVERT: B 93 THR cc_start: 0.8721 (m) cc_final: 0.8491 (p) REVERT: B 152 ILE cc_start: 0.8654 (tp) cc_final: 0.8377 (mt) REVERT: B 200 ILE cc_start: 0.8550 (OUTLIER) cc_final: 0.8271 (mm) REVERT: B 222 ARG cc_start: 0.6028 (mmm-85) cc_final: 0.5725 (mmm-85) REVERT: B 279 ARG cc_start: 0.7971 (mtm-85) cc_final: 0.7714 (ttm-80) outliers start: 27 outliers final: 18 residues processed: 140 average time/residue: 0.1952 time to fit residues: 33.4696 Evaluate side-chains 144 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.501 ------------------------------------------------------------------------------- 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 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 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 89 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 259 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 17 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 5 optimal weight: 0.0060 chunk 22 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.7000 ------------------------------------------------------------------------------- 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 A 299 GLN B 28 ASN ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 ASN B 110 GLN 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 = 0.4239 r_free = 0.4239 target = 0.161018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.147839 restraints weight = 9755.522| |-----------------------------------------------------------------------------| r_work (start): 0.4056 rms_B_bonded: 3.64 r_work: 0.3942 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4785 Z= 0.220 Angle : 0.595 7.187 6509 Z= 0.306 Chirality : 0.043 0.143 740 Planarity : 0.004 0.051 848 Dihedral : 4.813 46.170 653 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.80 % Favored : 95.87 % Rotamer: Outliers : 5.43 % Allowed : 21.32 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.33), residues: 606 helix: 0.37 (0.42), residues: 166 sheet: -1.54 (0.49), residues: 88 loop : -0.81 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 207 HIS 0.003 0.001 HIS B 41 PHE 0.015 0.001 PHE A 230 TYR 0.011 0.001 TYR A 101 ARG 0.002 0.000 ARG A 4 *********************** 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 155 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 0.531 Fit side-chains revert: symmetry clash REVERT: A 77 VAL cc_start: 0.5420 (OUTLIER) cc_final: 0.5032 (m) REVERT: A 119 ASN cc_start: 0.8530 (t0) cc_final: 0.8285 (t0) REVERT: A 222 ARG cc_start: 0.6090 (mmm-85) cc_final: 0.5830 (mmm-85) REVERT: A 247 VAL cc_start: 0.4520 (OUTLIER) cc_final: 0.4305 (p) REVERT: B 49 MET cc_start: 0.5406 (tpp) cc_final: 0.5007 (tpt) REVERT: B 93 THR cc_start: 0.8746 (m) cc_final: 0.8504 (p) REVERT: B 110 GLN cc_start: 0.8264 (mt0) cc_final: 0.8026 (mt0) REVERT: B 152 ILE cc_start: 0.8700 (tp) cc_final: 0.8439 (mt) REVERT: B 222 ARG cc_start: 0.6128 (mmm-85) cc_final: 0.5838 (mmm-85) REVERT: B 279 ARG cc_start: 0.7986 (mtm-85) cc_final: 0.7754 (ttm-80) outliers start: 28 outliers final: 21 residues processed: 142 average time/residue: 0.1942 time to fit residues: 33.8431 Evaluate side-chains 146 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.528 ------------------------------------------------------------------------------- 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 50 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 ASN B 192 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.162145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.149066 restraints weight = 9662.866| |-----------------------------------------------------------------------------| r_work (start): 0.4073 rms_B_bonded: 3.54 r_work: 0.3959 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4785 Z= 0.238 Angle : 0.621 6.161 6509 Z= 0.323 Chirality : 0.043 0.140 740 Planarity : 0.004 0.051 848 Dihedral : 4.509 24.732 651 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.96 % Favored : 95.87 % Rotamer: Outliers : 6.01 % Allowed : 20.74 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.33), residues: 606 helix: 0.23 (0.41), residues: 166 sheet: -1.54 (0.52), residues: 80 loop : -0.85 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 207 HIS 0.003 0.001 HIS B 41 PHE 0.015 0.001 PHE A 230 TYR 0.012 0.001 TYR B 101 ARG 0.002 0.000 ARG B 4 *********************** 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 159 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 128 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 ASN cc_start: 0.8487 (t0) cc_final: 0.8247 (t0) REVERT: A 222 ARG cc_start: 0.6134 (mmm-85) cc_final: 0.5859 (mmm-85) REVERT: A 247 VAL cc_start: 0.4572 (OUTLIER) cc_final: 0.4352 (p) REVERT: A 259 ILE cc_start: 0.8628 (mm) cc_final: 0.8423 (mm) REVERT: B 49 MET cc_start: 0.5473 (tpp) cc_final: 0.5060 (tpt) REVERT: B 85 CYS cc_start: 0.8896 (t) cc_final: 0.8501 (t) REVERT: B 93 THR cc_start: 0.8728 (m) cc_final: 0.8479 (p) REVERT: B 222 ARG cc_start: 0.6378 (mmm-85) cc_final: 0.6052 (mmm-85) outliers start: 31 outliers final: 23 residues processed: 145 average time/residue: 0.1912 time to fit residues: 34.0123 Evaluate side-chains 149 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.551 ------------------------------------------------------------------------------- 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 50 LEU Chi-restraints excluded: chain A residue 53 ASN 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 130 MET 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 181 PHE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 243 THR 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 9 optimal weight: 0.1980 chunk 55 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 43 optimal weight: 0.3980 chunk 53 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 21 optimal weight: 0.0050 chunk 19 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 overall best weight: 0.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 ASN B 110 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.164176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.151148 restraints weight = 9680.945| |-----------------------------------------------------------------------------| r_work (start): 0.4097 rms_B_bonded: 3.60 r_work: 0.3984 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4785 Z= 0.185 Angle : 0.615 6.440 6509 Z= 0.313 Chirality : 0.042 0.133 740 Planarity : 0.004 0.053 848 Dihedral : 4.382 27.741 651 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 5.23 % Allowed : 20.54 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.33), residues: 606 helix: 0.40 (0.42), residues: 166 sheet: -1.54 (0.52), residues: 80 loop : -0.79 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 31 HIS 0.002 0.001 HIS A 41 PHE 0.007 0.001 PHE A 230 TYR 0.010 0.001 TYR B 101 ARG 0.001 0.000 ARG A 4 *********************** 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 153 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 126 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASN cc_start: 0.8453 (t0) cc_final: 0.8197 (t0) REVERT: A 222 ARG cc_start: 0.6093 (mmm-85) cc_final: 0.5842 (mmm-85) REVERT: B 49 MET cc_start: 0.5358 (tpp) cc_final: 0.4922 (tpt) REVERT: B 93 THR cc_start: 0.8750 (m) cc_final: 0.8545 (p) REVERT: B 222 ARG cc_start: 0.6406 (mmm-85) cc_final: 0.6099 (mmm-85) outliers start: 27 outliers final: 24 residues processed: 143 average time/residue: 0.1868 time to fit residues: 32.9029 Evaluate side-chains 145 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 0.484 ------------------------------------------------------------------------------- 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 50 LEU Chi-restraints excluded: chain A residue 53 ASN Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 89 LEU 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 B residue 32 LEU Chi-restraints excluded: chain B residue 53 ASN 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 117 CYS Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 181 PHE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 36 optimal weight: 0.0970 chunk 16 optimal weight: 1.9990 chunk 9 optimal weight: 0.1980 chunk 56 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 46 optimal weight: 0.0770 chunk 1 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 overall best weight: 0.3736 ------------------------------------------------------------------------------- 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 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 ASN B 110 GLN B 164 HIS B 192 GLN B 203 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.164722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.151564 restraints weight = 9793.086| |-----------------------------------------------------------------------------| r_work (start): 0.4102 rms_B_bonded: 3.60 r_work: 0.3989 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.3614 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= 0.190 Angle : 0.632 6.711 6509 Z= 0.321 Chirality : 0.042 0.126 740 Planarity : 0.004 0.052 848 Dihedral : 4.279 27.681 651 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.46 % Allowed : 21.12 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.33), residues: 606 helix: 0.45 (0.41), residues: 166 sheet: -1.61 (0.51), residues: 80 loop : -0.77 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 31 HIS 0.002 0.001 HIS A 41 PHE 0.008 0.001 PHE A 230 TYR 0.013 0.001 TYR A 239 ARG 0.001 0.000 ARG A 4 *********************** 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 147 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASN cc_start: 0.8518 (t0) cc_final: 0.8255 (t0) REVERT: A 166 GLU cc_start: 0.8532 (tp30) cc_final: 0.8269 (tp30) REVERT: A 222 ARG cc_start: 0.6176 (mmm-85) cc_final: 0.5936 (mmm-85) REVERT: B 5 LYS cc_start: 0.8896 (tmtt) cc_final: 0.8684 (tmtt) REVERT: B 49 MET cc_start: 0.5269 (tpp) cc_final: 0.4858 (tpt) REVERT: B 85 CYS cc_start: 0.8841 (t) cc_final: 0.8452 (t) REVERT: B 222 ARG cc_start: 0.6413 (mmm-85) cc_final: 0.6112 (mmm-85) outliers start: 23 outliers final: 20 residues processed: 139 average time/residue: 0.1923 time to fit residues: 32.8171 Evaluate side-chains 139 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.508 ------------------------------------------------------------------------------- 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 50 LEU Chi-restraints excluded: chain A residue 53 ASN 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 196 THR Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 53 ASN 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 6 optimal weight: 0.5980 chunk 19 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 25 optimal weight: 0.0170 chunk 20 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 24 optimal weight: 0.4980 chunk 31 optimal weight: 4.9990 overall best weight: 0.5420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 ASN B 110 GLN B 164 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.163394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.150194 restraints weight = 9708.974| |-----------------------------------------------------------------------------| r_work (start): 0.4082 rms_B_bonded: 3.59 r_work: 0.3968 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4785 Z= 0.213 Angle : 0.661 9.447 6509 Z= 0.338 Chirality : 0.042 0.131 740 Planarity : 0.004 0.051 848 Dihedral : 4.317 25.398 651 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.46 % Allowed : 21.32 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.33), residues: 606 helix: 0.44 (0.42), residues: 166 sheet: -1.61 (0.51), residues: 80 loop : -0.81 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 31 HIS 0.003 0.001 HIS B 164 PHE 0.012 0.001 PHE A 230 TYR 0.013 0.001 TYR B 101 ARG 0.002 0.000 ARG B 4 ********************** 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 145 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 TYR cc_start: 0.8204 (p90) cc_final: 0.7956 (p90) REVERT: A 119 ASN cc_start: 0.8515 (t0) cc_final: 0.8252 (t0) REVERT: A 152 ILE cc_start: 0.8481 (mt) cc_final: 0.8027 (tp) REVERT: A 166 GLU cc_start: 0.8571 (tp30) cc_final: 0.8262 (tp30) REVERT: A 222 ARG cc_start: 0.6159 (mmm-85) cc_final: 0.5921 (mmm-85) REVERT: B 49 MET cc_start: 0.5362 (tpp) cc_final: 0.4927 (tpt) REVERT: B 85 CYS cc_start: 0.8859 (t) cc_final: 0.8419 (t) REVERT: B 222 ARG cc_start: 0.6397 (mmm-85) cc_final: 0.6115 (mmm-85) outliers start: 23 outliers final: 22 residues processed: 136 average time/residue: 0.2010 time to fit residues: 33.5462 Evaluate side-chains 142 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.501 ------------------------------------------------------------------------------- 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 50 LEU Chi-restraints excluded: chain A residue 53 ASN Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 89 LEU 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 B residue 32 LEU Chi-restraints excluded: chain B residue 53 ASN 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 164 HIS Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 181 PHE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 29 optimal weight: 0.9990 chunk 24 optimal weight: 0.0570 chunk 59 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 30 optimal weight: 0.0980 chunk 5 optimal weight: 0.1980 chunk 51 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 overall best weight: 0.4298 ------------------------------------------------------------------------------- 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 83 GLN B 84 ASN B 110 GLN B 164 HIS B 192 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.163879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.150729 restraints weight = 9690.424| |-----------------------------------------------------------------------------| r_work (start): 0.4090 rms_B_bonded: 3.59 r_work: 0.3976 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4785 Z= 0.201 Angle : 0.642 6.900 6509 Z= 0.327 Chirality : 0.042 0.128 740 Planarity : 0.004 0.051 848 Dihedral : 4.315 26.873 651 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 5.23 % Allowed : 20.35 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.33), residues: 606 helix: 0.44 (0.41), residues: 166 sheet: -1.53 (0.51), residues: 80 loop : -0.81 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 31 HIS 0.007 0.001 HIS B 164 PHE 0.010 0.001 PHE A 230 TYR 0.013 0.001 TYR A 239 ARG 0.002 0.000 ARG A 4 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2514.63 seconds wall clock time: 43 minutes 53.87 seconds (2633.87 seconds total)