Starting phenix.real_space_refine on Fri Dec 27 12:25:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eke_28200/12_2024/8eke_28200.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eke_28200/12_2024/8eke_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_28200/12_2024/8eke_28200.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eke_28200/12_2024/8eke_28200.map" model { file = "/net/cci-nas-00/data/ceres_data/8eke_28200/12_2024/8eke_28200.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eke_28200/12_2024/8eke_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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 3.84, 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: 1.07 Conformation dependent library (CDL) restraints added in 593.8 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: 0.55 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: 1.20 Time building geometry restraints manager: 1.24 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: 1.600 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.870 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: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.730 ------------------------------------------------------------------------------- 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 : 0.691 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: 0.1952 time to fit residues: 37.2756 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 : 0.519 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 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 : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 MET cc_start: 0.8905 (tpp) cc_final: 0.8631 (ttm) REVERT: A 77 VAL cc_start: 0.5734 (OUTLIER) cc_final: 0.5340 (m) REVERT: A 207 TRP cc_start: 0.9010 (t60) cc_final: 0.8214 (t60) REVERT: A 222 ARG cc_start: 0.5734 (mmm-85) cc_final: 0.5454 (mmm-85) REVERT: B 91 VAL cc_start: 0.4663 (OUTLIER) cc_final: 0.4419 (p) REVERT: B 93 THR cc_start: 0.8756 (m) cc_final: 0.8452 (p) REVERT: B 110 GLN cc_start: 0.8412 (mt0) cc_final: 0.8203 (mt0) REVERT: B 152 ILE cc_start: 0.8756 (tp) cc_final: 0.8493 (mt) REVERT: B 222 ARG cc_start: 0.5896 (mmm-85) cc_final: 0.5594 (mmm-85) REVERT: B 238 ASN cc_start: 0.7530 (t0) cc_final: 0.7257 (t0) outliers start: 33 outliers final: 16 residues processed: 145 average time/residue: 0.1899 time to fit residues: 33.9090 Evaluate side-chains 138 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.499 ------------------------------------------------------------------------------- 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 268 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 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 30 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 58 optimal weight: 0.4980 chunk 48 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.2482 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= 0.215 Angle : 0.595 11.073 6509 Z= 0.303 Chirality : 0.042 0.136 740 Planarity : 0.004 0.051 848 Dihedral : 4.832 45.285 653 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.96 % Favored : 95.71 % Rotamer: Outliers : 5.43 % Allowed : 19.19 % 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 (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: -0.75 (0.33), residues: 606 helix: 0.41 (0.42), residues: 166 sheet: -1.21 (0.49), residues: 82 loop : -0.72 (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 0.015 0.001 PHE A 230 TYR 0.018 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 151 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 123 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 VAL cc_start: 0.5724 (OUTLIER) cc_final: 0.5303 (m) REVERT: A 152 ILE cc_start: 0.8614 (tp) cc_final: 0.8314 (mt) REVERT: A 222 ARG cc_start: 0.5711 (mmm-85) cc_final: 0.5417 (mmm-85) REVERT: B 17 MET cc_start: 0.8808 (tpp) cc_final: 0.8437 (ttp) REVERT: B 91 VAL cc_start: 0.4518 (OUTLIER) cc_final: 0.4217 (p) REVERT: B 93 THR cc_start: 0.8783 (m) cc_final: 0.8469 (p) REVERT: B 102 LYS cc_start: 0.8457 (mmmm) cc_final: 0.8193 (mmmt) REVERT: B 152 ILE cc_start: 0.8749 (tp) cc_final: 0.8438 (mt) REVERT: B 222 ARG cc_start: 0.5878 (mmm-85) cc_final: 0.5571 (mmm-85) outliers start: 28 outliers final: 18 residues processed: 140 average time/residue: 0.1953 time to fit residues: 33.4327 Evaluate side-chains 142 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 0.493 ------------------------------------------------------------------------------- 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 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 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 41 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 36 optimal weight: 0.0170 chunk 54 optimal weight: 0.0060 chunk 57 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 48 optimal weight: 0.3980 chunk 32 optimal weight: 0.9990 overall best weight: 0.3434 ------------------------------------------------------------------------------- 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 192 GLN B 299 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 4785 Z= 0.163 Angle : 0.557 8.614 6509 Z= 0.277 Chirality : 0.041 0.149 740 Planarity : 0.004 0.054 848 Dihedral : 4.604 44.022 653 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.13 % Favored : 95.54 % Rotamer: Outliers : 4.26 % Allowed : 20.54 % 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: -0.47 (0.33), residues: 606 helix: 1.05 (0.44), residues: 154 sheet: -1.05 (0.47), residues: 100 loop : -0.67 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 207 HIS 0.003 0.001 HIS A 172 PHE 0.006 0.001 PHE A 230 TYR 0.009 0.001 TYR A 101 ARG 0.001 0.000 ARG A 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 155 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 VAL cc_start: 0.5778 (OUTLIER) cc_final: 0.5345 (m) REVERT: A 119 ASN cc_start: 0.8388 (t0) cc_final: 0.8117 (t0) REVERT: A 152 ILE cc_start: 0.8523 (tp) cc_final: 0.8247 (mt) REVERT: A 222 ARG cc_start: 0.5581 (mmm-85) cc_final: 0.5330 (mmm-85) REVERT: B 93 THR cc_start: 0.8792 (m) cc_final: 0.8579 (p) REVERT: B 152 ILE cc_start: 0.8617 (tp) cc_final: 0.8364 (mt) REVERT: B 222 ARG cc_start: 0.5795 (mmm-85) cc_final: 0.5524 (mmm-85) outliers start: 22 outliers final: 15 residues processed: 144 average time/residue: 0.1985 time to fit residues: 34.9392 Evaluate side-chains 141 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 0.428 ------------------------------------------------------------------------------- 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 205 LEU Chi-restraints excluded: chain A residue 225 THR 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 235 MET Chi-restraints excluded: chain B residue 259 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 34 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4785 Z= 0.207 Angle : 0.592 7.698 6509 Z= 0.303 Chirality : 0.043 0.145 740 Planarity : 0.004 0.052 848 Dihedral : 4.763 45.124 653 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.63 % Favored : 96.04 % Rotamer: Outliers : 4.84 % Allowed : 20.74 % 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: -0.74 (0.33), residues: 606 helix: 0.59 (0.43), residues: 166 sheet: -1.51 (0.50), residues: 88 loop : -0.70 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 207 HIS 0.003 0.001 HIS A 172 PHE 0.015 0.001 PHE A 230 TYR 0.010 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 154 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 VAL cc_start: 0.5857 (OUTLIER) cc_final: 0.5429 (m) REVERT: A 119 ASN cc_start: 0.8426 (t0) cc_final: 0.8162 (t0) REVERT: A 152 ILE cc_start: 0.8538 (tp) cc_final: 0.8324 (mt) REVERT: A 222 ARG cc_start: 0.5648 (mmm-85) cc_final: 0.5382 (mmm-85) REVERT: B 83 GLN cc_start: 0.7488 (pp30) cc_final: 0.7239 (pp30) REVERT: B 93 THR cc_start: 0.8818 (m) cc_final: 0.8565 (p) REVERT: B 102 LYS cc_start: 0.8405 (mmmm) cc_final: 0.8146 (mmmt) REVERT: B 222 ARG cc_start: 0.5838 (mmm-85) cc_final: 0.5526 (mmm-85) outliers start: 25 outliers final: 21 residues processed: 143 average time/residue: 0.1972 time to fit residues: 34.5728 Evaluate side-chains 148 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 0.549 ------------------------------------------------------------------------------- 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 225 THR 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 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 14 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 chunk 6 optimal weight: 0.4980 chunk 33 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 ASN B 192 GLN B 299 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.3231 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= 0.210 Angle : 0.598 6.947 6509 Z= 0.307 Chirality : 0.042 0.143 740 Planarity : 0.004 0.051 848 Dihedral : 4.354 27.087 651 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.96 % Favored : 95.87 % Rotamer: Outliers : 5.43 % Allowed : 20.74 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.33), residues: 606 helix: 0.50 (0.42), residues: 166 sheet: -1.54 (0.50), residues: 88 loop : -0.71 (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 A 172 PHE 0.014 0.001 PHE A 230 TYR 0.011 0.001 TYR B 239 ARG 0.001 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 158 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 MET cc_start: 0.8842 (ttm) cc_final: 0.8567 (ttp) REVERT: A 77 VAL cc_start: 0.5860 (OUTLIER) cc_final: 0.5422 (m) REVERT: A 119 ASN cc_start: 0.8420 (t0) cc_final: 0.8148 (t0) REVERT: A 222 ARG cc_start: 0.5615 (mmm-85) cc_final: 0.5355 (mmm-85) REVERT: A 259 ILE cc_start: 0.8571 (mm) cc_final: 0.8344 (mm) REVERT: B 93 THR cc_start: 0.8822 (m) cc_final: 0.8563 (p) REVERT: B 222 ARG cc_start: 0.5833 (mmm-85) cc_final: 0.5552 (mmm-85) REVERT: B 279 ARG cc_start: 0.7904 (mtm-85) cc_final: 0.7658 (ttm-80) outliers start: 28 outliers final: 20 residues processed: 145 average time/residue: 0.1937 time to fit residues: 34.3187 Evaluate side-chains 146 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 0.557 ------------------------------------------------------------------------------- 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 57 optimal weight: 0.0030 chunk 36 optimal weight: 0.9980 chunk 35 optimal weight: 0.4980 chunk 26 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 chunk 11 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- 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 84 ASN B 192 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.3339 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= 0.195 Angle : 0.599 6.057 6509 Z= 0.308 Chirality : 0.042 0.138 740 Planarity : 0.004 0.052 848 Dihedral : 4.323 26.936 651 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.84 % Allowed : 21.32 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.33), residues: 606 helix: 0.49 (0.42), residues: 166 sheet: -1.55 (0.49), residues: 88 loop : -0.63 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 31 HIS 0.002 0.001 HIS B 41 PHE 0.011 0.001 PHE A 230 TYR 0.016 0.001 TYR A 239 ARG 0.001 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 150 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 VAL cc_start: 0.5859 (OUTLIER) cc_final: 0.5420 (m) REVERT: A 119 ASN cc_start: 0.8411 (t0) cc_final: 0.8132 (t0) REVERT: A 222 ARG cc_start: 0.5645 (mmm-85) cc_final: 0.5415 (mmm-85) REVERT: A 259 ILE cc_start: 0.8554 (mm) cc_final: 0.8350 (mm) REVERT: B 17 MET cc_start: 0.8872 (ttm) cc_final: 0.8610 (ttm) REVERT: B 85 CYS cc_start: 0.9085 (t) cc_final: 0.8714 (t) REVERT: B 93 THR cc_start: 0.8823 (m) cc_final: 0.8593 (p) REVERT: B 222 ARG cc_start: 0.5837 (mmm-85) cc_final: 0.5521 (mmm-85) REVERT: B 279 ARG cc_start: 0.7911 (mtm-85) cc_final: 0.7673 (ttm-80) outliers start: 25 outliers final: 21 residues processed: 140 average time/residue: 0.1972 time to fit residues: 33.6035 Evaluate side-chains 143 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 0.498 ------------------------------------------------------------------------------- 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 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 117 CYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN A 127 GLN A 164 HIS B 84 ASN B 110 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 4785 Z= 0.311 Angle : 0.694 6.478 6509 Z= 0.366 Chirality : 0.045 0.157 740 Planarity : 0.004 0.046 848 Dihedral : 4.884 27.823 651 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 5.04 % Allowed : 21.32 % Favored : 73.64 % 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: -1.07 (0.32), residues: 606 helix: 0.09 (0.41), residues: 166 sheet: -2.16 (0.66), residues: 56 loop : -0.83 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 207 HIS 0.004 0.001 HIS B 41 PHE 0.024 0.001 PHE A 230 TYR 0.008 0.002 TYR B 239 ARG 0.002 0.000 ARG B 279 *********************** 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 150 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 0.576 Fit side-chains revert: symmetry clash REVERT: B 17 MET cc_start: 0.8869 (ttm) cc_final: 0.8581 (ttm) REVERT: B 85 CYS cc_start: 0.9108 (t) cc_final: 0.8723 (t) REVERT: B 93 THR cc_start: 0.8808 (m) cc_final: 0.8493 (p) REVERT: B 222 ARG cc_start: 0.5930 (mmm-85) cc_final: 0.5625 (mmm-85) outliers start: 26 outliers final: 22 residues processed: 140 average time/residue: 0.2044 time to fit residues: 35.1067 Evaluate side-chains 144 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 0.499 ------------------------------------------------------------------------------- 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 130 MET Chi-restraints excluded: chain A residue 196 THR 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 91 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 0.0980 chunk 50 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 59 optimal weight: 0.4980 chunk 55 optimal weight: 0.0000 chunk 47 optimal weight: 0.9990 overall best weight: 0.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN A 119 ASN A 192 GLN B 84 ASN B 110 GLN B 192 GLN B 203 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.3679 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= 0.190 Angle : 0.644 6.652 6509 Z= 0.328 Chirality : 0.042 0.131 740 Planarity : 0.004 0.053 848 Dihedral : 4.465 26.459 651 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 4.26 % Allowed : 21.51 % 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: 0.39 (0.41), residues: 166 sheet: -1.60 (0.52), residues: 80 loop : -0.77 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 218 HIS 0.002 0.001 HIS A 41 PHE 0.008 0.001 PHE A 181 TYR 0.006 0.001 TYR B 101 ARG 0.002 0.000 ARG A 217 *********************** 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 143 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 85 CYS cc_start: 0.9112 (t) cc_final: 0.8691 (t) REVERT: B 93 THR cc_start: 0.8821 (m) cc_final: 0.8600 (p) REVERT: B 222 ARG cc_start: 0.5880 (mmm-85) cc_final: 0.5593 (mmm-85) outliers start: 22 outliers final: 19 residues processed: 133 average time/residue: 0.2017 time to fit residues: 32.6457 Evaluate side-chains 136 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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 89 LEU Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 42 VAL 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 91 VAL Chi-restraints excluded: chain B residue 117 CYS 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 4 optimal weight: 0.0570 chunk 36 optimal weight: 0.0770 chunk 29 optimal weight: 0.4980 chunk 37 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 14 optimal weight: 0.0270 chunk 43 optimal weight: 0.6980 chunk 7 optimal weight: 0.3980 chunk 13 optimal weight: 0.9980 chunk 47 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 overall best weight: 0.2114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN A 164 HIS B 84 ASN B 180 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.3833 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= 0.184 Angle : 0.641 6.933 6509 Z= 0.325 Chirality : 0.042 0.130 740 Planarity : 0.004 0.054 848 Dihedral : 4.304 26.168 651 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.10 % Allowed : 22.29 % Favored : 74.61 % 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: -0.53 (0.33), residues: 606 helix: 0.92 (0.43), residues: 154 sheet: -1.05 (0.44), residues: 104 loop : -0.67 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 218 HIS 0.002 0.001 HIS A 41 PHE 0.014 0.001 PHE A 181 TYR 0.012 0.001 TYR A 239 ARG 0.001 0.000 ARG B 60 ********************** 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 138 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4 ARG cc_start: 0.8628 (mmm-85) cc_final: 0.8401 (mmm-85) REVERT: B 222 ARG cc_start: 0.5917 (mmm-85) cc_final: 0.5644 (mmm-85) outliers start: 16 outliers final: 11 residues processed: 129 average time/residue: 0.2054 time to fit residues: 32.2038 Evaluate side-chains 129 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 268 LEU 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 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 48 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 41 optimal weight: 0.0670 chunk 2 optimal weight: 1.9990 chunk 34 optimal weight: 0.4980 chunk 54 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN ** A 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 GLN A 192 GLN B 84 ASN B 110 GLN B 180 ASN B 192 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.159230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.146351 restraints weight = 9568.451| |-----------------------------------------------------------------------------| r_work (start): 0.3985 rms_B_bonded: 3.39 r_work: 0.3882 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.3937 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= 0.225 Angle : 0.698 9.398 6509 Z= 0.358 Chirality : 0.043 0.145 740 Planarity : 0.004 0.051 848 Dihedral : 4.517 26.210 651 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.29 % Allowed : 22.67 % Favored : 74.03 % 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: -0.59 (0.33), residues: 606 helix: 0.89 (0.43), residues: 154 sheet: -1.55 (0.51), residues: 80 loop : -0.65 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 218 HIS 0.002 0.001 HIS A 41 PHE 0.015 0.001 PHE A 230 TYR 0.011 0.001 TYR B 154 ARG 0.005 0.000 ARG A 279 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1563.75 seconds wall clock time: 28 minutes 49.37 seconds (1729.37 seconds total)