Starting phenix.real_space_refine on Fri Dec 27 14:25:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s7d_19766/12_2024/8s7d_19766.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s7d_19766/12_2024/8s7d_19766.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8s7d_19766/12_2024/8s7d_19766.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s7d_19766/12_2024/8s7d_19766.map" model { file = "/net/cci-nas-00/data/ceres_data/8s7d_19766/12_2024/8s7d_19766.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s7d_19766/12_2024/8s7d_19766.cif" } resolution = 3.2 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= 0.122 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 31 5.16 5 C 3507 2.51 5 N 931 2.21 5 O 1019 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 5488 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 904 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 2, 'TRANS': 110} Chain breaks: 1 Chain: "B" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 914 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 2, 'TRANS': 111} Chain breaks: 1 Chain: "C" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1005 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain breaks: 2 Chain: "D" Number of atoms: 2665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2665 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 13, 'TRANS': 327} Chain breaks: 5 Time building chain proxies: 5.97, per 1000 atoms: 1.09 Number of scatterers: 5488 At special positions: 0 Unit cell: (92.105, 104.78, 95.485, 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 31 16.00 O 1019 8.00 N 931 7.00 C 3507 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: 1.27 Conformation dependent library (CDL) restraints added in 643.7 milliseconds 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1318 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 8 sheets defined 48.3% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 11 through 26 Processing helix chain 'A' and resid 44 through 51 Processing helix chain 'A' and resid 53 through 60 Processing helix chain 'A' and resid 76 through 90 Proline residue: A 82 - end of helix Processing helix chain 'A' and resid 98 through 110 Processing helix chain 'A' and resid 116 through 121 removed outlier: 3.803A pdb=" N GLN A 120 " --> pdb=" O GLU A 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 27 Processing helix chain 'B' and resid 44 through 52 Processing helix chain 'B' and resid 52 through 60 Processing helix chain 'B' and resid 76 through 90 Proline residue: B 82 - end of helix removed outlier: 3.578A pdb=" N GLN B 85 " --> pdb=" O GLU B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 110 Processing helix chain 'B' and resid 115 through 123 removed outlier: 4.009A pdb=" N PHE B 119 " --> pdb=" O GLU B 115 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU B 122 " --> pdb=" O CYS B 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 23 removed outlier: 4.618A pdb=" N GLN C 23 " --> pdb=" O GLU C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 32 removed outlier: 4.173A pdb=" N MET C 30 " --> pdb=" O THR C 26 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU C 32 " --> pdb=" O LYS C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 64 Processing helix chain 'C' and resid 86 through 93 Processing helix chain 'C' and resid 96 through 111 Processing helix chain 'C' and resid 112 through 128 Processing helix chain 'C' and resid 131 through 140 Processing helix chain 'C' and resid 146 through 157 Processing helix chain 'D' and resid 19 through 26 removed outlier: 3.842A pdb=" N LEU D 23 " --> pdb=" O SER D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 36 removed outlier: 4.059A pdb=" N PHE D 36 " --> pdb=" O ARG D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 46 Processing helix chain 'D' and resid 49 through 62 Processing helix chain 'D' and resid 83 through 92 Processing helix chain 'D' and resid 108 through 112 Processing helix chain 'D' and resid 129 through 138 Processing helix chain 'D' and resid 202 through 209 removed outlier: 3.596A pdb=" N LEU D 206 " --> pdb=" O GLU D 202 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL D 209 " --> pdb=" O GLN D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 244 removed outlier: 3.770A pdb=" N PHE D 243 " --> pdb=" O VAL D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 311 Processing helix chain 'D' and resid 340 through 349 Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 8 Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 36 Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 94 removed outlier: 4.696A pdb=" N VAL B 4 " --> pdb=" O CYS D 378 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG D 376 " --> pdb=" O ALA B 6 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 39 through 43 Processing sheet with id=AA5, first strand: chain 'D' and resid 174 through 180 removed outlier: 5.938A pdb=" N HIS D 100 " --> pdb=" O GLN D 144 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N LEU D 146 " --> pdb=" O HIS D 100 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL D 102 " --> pdb=" O LEU D 146 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ILE D 148 " --> pdb=" O VAL D 102 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N TYR D 104 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N THR D 150 " --> pdb=" O TYR D 104 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ALA D 106 " --> pdb=" O THR D 150 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL D 145 " --> pdb=" O LEU D 261 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU D 261 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N GLY D 147 " --> pdb=" O SER D 259 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 153 through 155 Processing sheet with id=AA7, first strand: chain 'D' and resid 191 through 193 removed outlier: 3.751A pdb=" N GLY D 274 " --> pdb=" O TYR D 225 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR D 225 " --> pdb=" O GLY D 274 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL D 219 " --> pdb=" O PHE D 280 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N VAL D 220 " --> pdb=" O ALA D 251 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N GLY D 253 " --> pdb=" O VAL D 220 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL D 222 " --> pdb=" O GLY D 253 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N VAL D 255 " --> pdb=" O VAL D 222 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N GLY D 224 " --> pdb=" O VAL D 255 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE D 363 " --> pdb=" O GLY D 252 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 354 through 359 254 hydrogen bonds defined for protein. 723 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: 1.58 Time building geometry restraints manager: 1.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1796 1.34 - 1.46: 1137 1.46 - 1.58: 2608 1.58 - 1.70: 0 1.70 - 1.82: 40 Bond restraints: 5581 Sorted by residual: bond pdb=" CB GLN A 120 " pdb=" CG GLN A 120 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.58e+00 bond pdb=" CB LYS D 141 " pdb=" CG LYS D 141 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.17e+00 bond pdb=" CB PHE A 108 " pdb=" CG PHE A 108 " ideal model delta sigma weight residual 1.502 1.526 -0.024 2.30e-02 1.89e+03 1.07e+00 bond pdb=" CB ARG D 86 " pdb=" CG ARG D 86 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.05e+00 bond pdb=" CB LYS D 347 " pdb=" CG LYS D 347 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.60e-01 ... (remaining 5576 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 7454 2.08 - 4.15: 61 4.15 - 6.23: 17 6.23 - 8.30: 1 8.30 - 10.38: 3 Bond angle restraints: 7536 Sorted by residual: angle pdb=" CA GLN A 120 " pdb=" CB GLN A 120 " pdb=" CG GLN A 120 " ideal model delta sigma weight residual 114.10 123.44 -9.34 2.00e+00 2.50e-01 2.18e+01 angle pdb=" CB MET D 306 " pdb=" CG MET D 306 " pdb=" SD MET D 306 " ideal model delta sigma weight residual 112.70 122.86 -10.16 3.00e+00 1.11e-01 1.15e+01 angle pdb=" CB LYS D 141 " pdb=" CG LYS D 141 " pdb=" CD LYS D 141 " ideal model delta sigma weight residual 111.30 118.36 -7.06 2.30e+00 1.89e-01 9.43e+00 angle pdb=" CA LEU C 55 " pdb=" CB LEU C 55 " pdb=" CG LEU C 55 " ideal model delta sigma weight residual 116.30 126.68 -10.38 3.50e+00 8.16e-02 8.79e+00 angle pdb=" CA LYS D 347 " pdb=" CB LYS D 347 " pdb=" CG LYS D 347 " ideal model delta sigma weight residual 114.10 119.90 -5.80 2.00e+00 2.50e-01 8.40e+00 ... (remaining 7531 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 2790 17.95 - 35.90: 388 35.90 - 53.85: 140 53.85 - 71.80: 30 71.80 - 89.75: 11 Dihedral angle restraints: 3359 sinusoidal: 1350 harmonic: 2009 Sorted by residual: dihedral pdb=" CA ASP D 107 " pdb=" C ASP D 107 " pdb=" N SER D 108 " pdb=" CA SER D 108 " ideal model delta harmonic sigma weight residual -180.00 -162.27 -17.73 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA ASP B 22 " pdb=" CB ASP B 22 " pdb=" CG ASP B 22 " pdb=" OD1 ASP B 22 " ideal model delta sinusoidal sigma weight residual -30.00 -89.15 59.15 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CA ASP C 17 " pdb=" CB ASP C 17 " pdb=" CG ASP C 17 " pdb=" OD1 ASP C 17 " ideal model delta sinusoidal sigma weight residual -30.00 -87.66 57.66 1 2.00e+01 2.50e-03 1.12e+01 ... (remaining 3356 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 498 0.027 - 0.054: 228 0.054 - 0.081: 81 0.081 - 0.108: 59 0.108 - 0.136: 16 Chirality restraints: 882 Sorted by residual: chirality pdb=" CA ILE D 374 " pdb=" N ILE D 374 " pdb=" C ILE D 374 " pdb=" CB ILE D 374 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.59e-01 chirality pdb=" CA VAL D 276 " pdb=" N VAL D 276 " pdb=" C VAL D 276 " pdb=" CB VAL D 276 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.98e-01 chirality pdb=" CG LEU C 55 " pdb=" CB LEU C 55 " pdb=" CD1 LEU C 55 " pdb=" CD2 LEU C 55 " both_signs ideal model delta sigma weight residual False -2.59 -2.47 -0.12 2.00e-01 2.50e+01 3.88e-01 ... (remaining 879 not shown) Planarity restraints: 957 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 156 " 0.040 5.00e-02 4.00e+02 6.05e-02 5.86e+00 pdb=" N PRO D 157 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO D 157 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 157 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 120 " -0.010 2.00e-02 2.50e+03 1.94e-02 3.76e+00 pdb=" C GLN A 120 " 0.034 2.00e-02 2.50e+03 pdb=" O GLN A 120 " -0.013 2.00e-02 2.50e+03 pdb=" N PHE A 121 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 108 " -0.010 2.00e-02 2.50e+03 1.28e-02 2.86e+00 pdb=" CG PHE B 108 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE B 108 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE B 108 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE B 108 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 108 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 108 " -0.000 2.00e-02 2.50e+03 ... (remaining 954 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 81 2.65 - 3.21: 5018 3.21 - 3.78: 8590 3.78 - 4.34: 11768 4.34 - 4.90: 19382 Nonbonded interactions: 44839 Sorted by model distance: nonbonded pdb=" O GLN B 85 " pdb=" OG1 THR B 89 " model vdw 2.090 3.040 nonbonded pdb=" OD1 ASP D 107 " pdb=" OG1 THR D 110 " model vdw 2.194 3.040 nonbonded pdb=" O THR C 26 " pdb=" OG1 THR C 29 " model vdw 2.198 3.040 nonbonded pdb=" OG SER D 173 " pdb=" N GLY D 174 " model vdw 2.291 3.120 nonbonded pdb=" ND2 ASN A 15 " pdb=" OD1 ASN B 113 " model vdw 2.295 3.120 ... (remaining 44834 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 4 through 60 or resid 69 through 122)) selection = (chain 'B' and (resid 4 through 60 or resid 69 through 122)) } 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: 0.640 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 18.670 Find NCS groups from input model: 0.110 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 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 : 0.003 0.038 5581 Z= 0.166 Angle : 0.569 10.379 7536 Z= 0.297 Chirality : 0.042 0.136 882 Planarity : 0.004 0.061 957 Dihedral : 19.447 89.753 2041 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 4.70 % Allowed : 33.23 % Favored : 62.07 % 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: -0.33 (0.34), residues: 665 helix: 0.72 (0.31), residues: 296 sheet: -2.22 (0.53), residues: 98 loop : -0.29 (0.40), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 68 HIS 0.003 0.001 HIS D 398 PHE 0.029 0.001 PHE B 108 TYR 0.009 0.001 TYR A 88 ARG 0.008 0.000 ARG D 58 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 66 time to evaluate : 0.622 Fit side-chains REVERT: A 116 GLU cc_start: 0.3903 (mm-30) cc_final: 0.3150 (mt-10) outliers start: 29 outliers final: 27 residues processed: 92 average time/residue: 0.2154 time to fit residues: 25.1074 Evaluate side-chains 91 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 64 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 105 CYS Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 157 ASN Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 105 MET Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 144 GLN Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 188 GLN Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 287 SER Chi-restraints excluded: chain D residue 366 ASP Chi-restraints excluded: chain D residue 370 THR Chi-restraints excluded: chain D residue 383 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 57 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 28 optimal weight: 8.9990 chunk 17 optimal weight: 10.0000 chunk 34 optimal weight: 0.3980 chunk 27 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 32 optimal weight: 20.0000 chunk 39 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 HIS ** D 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5581 Z= 0.281 Angle : 0.577 7.450 7536 Z= 0.304 Chirality : 0.044 0.154 882 Planarity : 0.004 0.063 957 Dihedral : 8.174 77.559 773 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 5.19 % Allowed : 30.47 % Favored : 64.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.34), residues: 665 helix: 0.55 (0.30), residues: 296 sheet: -2.47 (0.52), residues: 97 loop : -0.43 (0.40), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 68 HIS 0.006 0.001 HIS B 56 PHE 0.012 0.001 PHE A 121 TYR 0.016 0.002 TYR D 104 ARG 0.005 0.001 ARG C 136 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 66 time to evaluate : 0.621 Fit side-chains revert: symmetry clash REVERT: A 93 ILE cc_start: 0.8011 (OUTLIER) cc_final: 0.7770 (mm) REVERT: A 115 GLU cc_start: 0.6377 (OUTLIER) cc_final: 0.4373 (mp0) REVERT: B 48 LEU cc_start: 0.7153 (OUTLIER) cc_final: 0.6511 (mp) REVERT: B 93 ILE cc_start: 0.7276 (OUTLIER) cc_final: 0.7044 (mp) REVERT: C 30 MET cc_start: 0.5998 (pmm) cc_final: 0.5373 (pmm) REVERT: D 58 ARG cc_start: 0.7973 (ttp-110) cc_final: 0.7482 (ttp-110) REVERT: D 105 MET cc_start: 0.7331 (OUTLIER) cc_final: 0.7102 (mtm) REVERT: D 148 ILE cc_start: 0.8009 (OUTLIER) cc_final: 0.7744 (mm) REVERT: D 213 ASP cc_start: 0.8155 (OUTLIER) cc_final: 0.7392 (t70) REVERT: D 347 LYS cc_start: 0.6330 (tptp) cc_final: 0.5290 (ttpt) outliers start: 32 outliers final: 20 residues processed: 91 average time/residue: 0.2459 time to fit residues: 27.5138 Evaluate side-chains 90 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 63 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 30 CYS Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 105 MET Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 148 ILE Chi-restraints excluded: chain D residue 188 GLN Chi-restraints excluded: chain D residue 193 ILE Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 284 ARG Chi-restraints excluded: chain D residue 287 SER Chi-restraints excluded: chain D residue 329 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 34 optimal weight: 6.9990 chunk 19 optimal weight: 8.9990 chunk 51 optimal weight: 0.9980 chunk 42 optimal weight: 7.9990 chunk 17 optimal weight: 30.0000 chunk 61 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 21 optimal weight: 7.9990 chunk 49 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 5581 Z= 0.388 Angle : 0.637 7.483 7536 Z= 0.334 Chirality : 0.047 0.154 882 Planarity : 0.005 0.065 957 Dihedral : 7.364 56.999 746 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 7.29 % Allowed : 28.53 % Favored : 64.18 % 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: 665 helix: 0.26 (0.30), residues: 296 sheet: -2.91 (0.50), residues: 99 loop : -0.55 (0.40), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 159 HIS 0.008 0.001 HIS B 56 PHE 0.016 0.002 PHE D 322 TYR 0.021 0.002 TYR D 104 ARG 0.007 0.000 ARG D 44 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 61 time to evaluate : 0.633 Fit side-chains REVERT: A 93 ILE cc_start: 0.8019 (OUTLIER) cc_final: 0.7768 (mm) REVERT: A 94 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7441 (mt) REVERT: A 115 GLU cc_start: 0.6453 (OUTLIER) cc_final: 0.4448 (mp0) REVERT: B 8 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8217 (tp30) REVERT: B 48 LEU cc_start: 0.7136 (OUTLIER) cc_final: 0.6471 (mp) REVERT: C 30 MET cc_start: 0.6095 (pmm) cc_final: 0.5457 (pmm) REVERT: D 105 MET cc_start: 0.7480 (OUTLIER) cc_final: 0.7148 (mtm) REVERT: D 148 ILE cc_start: 0.8251 (OUTLIER) cc_final: 0.8019 (mm) REVERT: D 178 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8117 (mt) REVERT: D 213 ASP cc_start: 0.8188 (OUTLIER) cc_final: 0.7437 (t70) REVERT: D 347 LYS cc_start: 0.6439 (tptp) cc_final: 0.5447 (ttpt) outliers start: 45 outliers final: 25 residues processed: 98 average time/residue: 0.2342 time to fit residues: 28.5711 Evaluate side-chains 95 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 61 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 30 CYS Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 105 MET Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 144 GLN Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 148 ILE Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 193 ILE Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 284 ARG Chi-restraints excluded: chain D residue 287 SER Chi-restraints excluded: chain D residue 370 THR Chi-restraints excluded: chain D residue 396 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 32 optimal weight: 7.9990 chunk 6 optimal weight: 0.1980 chunk 29 optimal weight: 9.9990 chunk 41 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 17 optimal weight: 6.9990 chunk 54 optimal weight: 10.0000 chunk 37 optimal weight: 0.4980 chunk 0 optimal weight: 20.0000 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 HIS ** D 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5581 Z= 0.166 Angle : 0.513 7.147 7536 Z= 0.268 Chirality : 0.043 0.156 882 Planarity : 0.004 0.061 957 Dihedral : 6.513 59.057 742 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 4.54 % Allowed : 30.63 % Favored : 64.83 % 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: -0.61 (0.33), residues: 665 helix: 0.55 (0.30), residues: 302 sheet: -2.70 (0.50), residues: 99 loop : -0.39 (0.40), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 68 HIS 0.003 0.001 HIS A 112 PHE 0.010 0.001 PHE A 121 TYR 0.015 0.001 TYR A 88 ARG 0.005 0.000 ARG D 44 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 74 time to evaluate : 0.758 Fit side-chains REVERT: A 115 GLU cc_start: 0.6198 (OUTLIER) cc_final: 0.4122 (mp0) REVERT: C 30 MET cc_start: 0.6094 (OUTLIER) cc_final: 0.5461 (pmm) REVERT: D 58 ARG cc_start: 0.7974 (ttp-110) cc_final: 0.7699 (ttp-110) REVERT: D 82 HIS cc_start: 0.5424 (OUTLIER) cc_final: 0.5037 (t-90) REVERT: D 148 ILE cc_start: 0.7914 (OUTLIER) cc_final: 0.7667 (mm) REVERT: D 213 ASP cc_start: 0.8192 (OUTLIER) cc_final: 0.7431 (t70) REVERT: D 347 LYS cc_start: 0.6263 (tptp) cc_final: 0.5410 (ttpt) outliers start: 28 outliers final: 14 residues processed: 97 average time/residue: 0.2635 time to fit residues: 31.1704 Evaluate side-chains 90 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 30 CYS Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 30 MET Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain D residue 82 HIS Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 148 ILE Chi-restraints excluded: chain D residue 193 ILE Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 284 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 1.9990 chunk 27 optimal weight: 0.3980 chunk 56 optimal weight: 0.6980 chunk 45 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 33 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 16 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 HIS ** D 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5581 Z= 0.203 Angle : 0.522 6.788 7536 Z= 0.273 Chirality : 0.043 0.167 882 Planarity : 0.004 0.060 957 Dihedral : 5.702 54.320 736 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 4.86 % Allowed : 31.28 % Favored : 63.86 % 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: -0.52 (0.33), residues: 665 helix: 0.64 (0.30), residues: 302 sheet: -2.69 (0.49), residues: 99 loop : -0.33 (0.40), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 68 HIS 0.003 0.001 HIS D 398 PHE 0.022 0.001 PHE A 108 TYR 0.013 0.001 TYR A 88 ARG 0.007 0.000 ARG D 44 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 73 time to evaluate : 0.539 Fit side-chains REVERT: A 115 GLU cc_start: 0.6258 (OUTLIER) cc_final: 0.4249 (mp0) REVERT: C 30 MET cc_start: 0.6107 (OUTLIER) cc_final: 0.5477 (pmm) REVERT: D 82 HIS cc_start: 0.5540 (OUTLIER) cc_final: 0.5286 (t-90) REVERT: D 213 ASP cc_start: 0.8212 (OUTLIER) cc_final: 0.7465 (t70) REVERT: D 347 LYS cc_start: 0.6322 (tptp) cc_final: 0.5504 (ttpt) outliers start: 30 outliers final: 20 residues processed: 98 average time/residue: 0.2504 time to fit residues: 29.9092 Evaluate side-chains 94 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 70 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 30 CYS Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 30 MET Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain D residue 82 HIS Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 193 ILE Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 284 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 38 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 34 optimal weight: 8.9990 chunk 63 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 37 optimal weight: 4.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 HIS ** D 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5581 Z= 0.251 Angle : 0.557 7.700 7536 Z= 0.290 Chirality : 0.044 0.176 882 Planarity : 0.004 0.061 957 Dihedral : 5.617 54.026 734 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 5.19 % Allowed : 30.47 % Favored : 64.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.33), residues: 665 helix: 0.58 (0.30), residues: 302 sheet: -2.74 (0.49), residues: 99 loop : -0.34 (0.40), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 68 HIS 0.005 0.001 HIS B 56 PHE 0.019 0.001 PHE B 108 TYR 0.013 0.002 TYR D 104 ARG 0.011 0.000 ARG D 44 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 67 time to evaluate : 0.612 Fit side-chains REVERT: A 115 GLU cc_start: 0.6368 (OUTLIER) cc_final: 0.4373 (mp0) REVERT: C 30 MET cc_start: 0.5961 (OUTLIER) cc_final: 0.5351 (pmm) REVERT: C 148 GLU cc_start: 0.7941 (pm20) cc_final: 0.7722 (pm20) REVERT: D 82 HIS cc_start: 0.5541 (OUTLIER) cc_final: 0.4900 (t70) REVERT: D 178 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8026 (mt) REVERT: D 202 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6785 (mp0) REVERT: D 213 ASP cc_start: 0.8225 (OUTLIER) cc_final: 0.7471 (t70) REVERT: D 347 LYS cc_start: 0.6304 (tptp) cc_final: 0.5458 (ttpt) outliers start: 32 outliers final: 24 residues processed: 93 average time/residue: 0.2344 time to fit residues: 27.2543 Evaluate side-chains 93 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 63 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 30 CYS Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 30 MET Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain D residue 82 HIS Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 193 ILE Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 284 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 chunk 55 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 39 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 19 optimal weight: 10.0000 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 HIS A 120 GLN ** D 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5581 Z= 0.235 Angle : 0.549 8.237 7536 Z= 0.286 Chirality : 0.044 0.184 882 Planarity : 0.004 0.060 957 Dihedral : 5.582 54.023 734 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 5.35 % Allowed : 30.79 % Favored : 63.86 % 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: 665 helix: 0.60 (0.30), residues: 303 sheet: -2.73 (0.49), residues: 99 loop : -0.31 (0.40), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 68 HIS 0.004 0.001 HIS B 56 PHE 0.026 0.002 PHE A 108 TYR 0.013 0.002 TYR A 88 ARG 0.009 0.000 ARG D 44 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 66 time to evaluate : 0.621 Fit side-chains REVERT: A 104 LYS cc_start: 0.6189 (tmtt) cc_final: 0.5882 (tmtt) REVERT: A 115 GLU cc_start: 0.6403 (OUTLIER) cc_final: 0.4383 (mp0) REVERT: C 30 MET cc_start: 0.5989 (OUTLIER) cc_final: 0.5388 (pmm) REVERT: D 82 HIS cc_start: 0.5624 (OUTLIER) cc_final: 0.5142 (t-90) REVERT: D 178 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.7990 (mt) REVERT: D 213 ASP cc_start: 0.8216 (OUTLIER) cc_final: 0.7464 (t70) REVERT: D 347 LYS cc_start: 0.6334 (tptp) cc_final: 0.5489 (ttpt) outliers start: 33 outliers final: 26 residues processed: 93 average time/residue: 0.2334 time to fit residues: 26.9851 Evaluate side-chains 92 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 61 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 30 CYS Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 30 MET Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 82 HIS Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 193 ILE Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 284 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 12 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 32 optimal weight: 7.9990 chunk 6 optimal weight: 0.0010 chunk 51 optimal weight: 0.5980 chunk 59 optimal weight: 0.0470 chunk 62 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 overall best weight: 0.3884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 HIS ** D 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6844 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5581 Z= 0.148 Angle : 0.519 10.071 7536 Z= 0.267 Chirality : 0.043 0.195 882 Planarity : 0.004 0.059 957 Dihedral : 5.325 54.642 734 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.89 % Allowed : 32.41 % Favored : 63.70 % 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: -0.23 (0.34), residues: 665 helix: 0.84 (0.30), residues: 301 sheet: -2.47 (0.48), residues: 98 loop : -0.19 (0.41), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 68 HIS 0.003 0.001 HIS A 112 PHE 0.021 0.001 PHE A 108 TYR 0.013 0.001 TYR A 88 ARG 0.005 0.000 ARG D 44 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 80 time to evaluate : 0.608 Fit side-chains REVERT: A 54 TYR cc_start: 0.6827 (t80) cc_final: 0.6484 (t80) REVERT: C 30 MET cc_start: 0.5954 (OUTLIER) cc_final: 0.5355 (pmm) REVERT: D 58 ARG cc_start: 0.7906 (ttp-110) cc_final: 0.7215 (mtm-85) REVERT: D 82 HIS cc_start: 0.5386 (OUTLIER) cc_final: 0.4767 (t-90) REVERT: D 213 ASP cc_start: 0.8168 (OUTLIER) cc_final: 0.7443 (t70) REVERT: D 347 LYS cc_start: 0.6129 (tptp) cc_final: 0.5369 (ttpt) outliers start: 24 outliers final: 19 residues processed: 99 average time/residue: 0.2665 time to fit residues: 31.9801 Evaluate side-chains 98 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 76 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 30 CYS Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 30 MET Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 82 HIS Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 193 ILE Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 284 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 26 optimal weight: 30.0000 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 39 optimal weight: 0.3980 chunk 30 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 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 112 HIS A 120 GLN ** D 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5581 Z= 0.185 Angle : 0.534 7.828 7536 Z= 0.279 Chirality : 0.043 0.192 882 Planarity : 0.004 0.059 957 Dihedral : 5.351 54.365 734 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 4.70 % Allowed : 31.93 % Favored : 63.37 % 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: -0.20 (0.34), residues: 665 helix: 0.88 (0.31), residues: 301 sheet: -2.42 (0.48), residues: 98 loop : -0.21 (0.41), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 68 HIS 0.003 0.001 HIS D 398 PHE 0.020 0.001 PHE B 108 TYR 0.012 0.001 TYR A 88 ARG 0.008 0.000 ARG D 44 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 72 time to evaluate : 0.617 Fit side-chains REVERT: A 54 TYR cc_start: 0.6827 (t80) cc_final: 0.6514 (t80) REVERT: A 58 ARG cc_start: 0.5869 (mmm160) cc_final: 0.5544 (mmm-85) REVERT: C 30 MET cc_start: 0.5969 (OUTLIER) cc_final: 0.5353 (pmm) REVERT: C 56 LYS cc_start: 0.8448 (tmmt) cc_final: 0.8062 (tptp) REVERT: D 58 ARG cc_start: 0.7917 (ttp-110) cc_final: 0.7248 (mtm-85) REVERT: D 82 HIS cc_start: 0.5555 (OUTLIER) cc_final: 0.4934 (t70) REVERT: D 213 ASP cc_start: 0.8188 (OUTLIER) cc_final: 0.7462 (t70) REVERT: D 347 LYS cc_start: 0.6168 (tptp) cc_final: 0.5394 (ttpt) outliers start: 29 outliers final: 21 residues processed: 95 average time/residue: 0.2296 time to fit residues: 27.2071 Evaluate side-chains 95 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 71 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 30 CYS Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 30 MET Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 82 HIS Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 193 ILE Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 284 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 67 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 42 optimal weight: 8.9990 chunk 57 optimal weight: 0.9980 chunk 16 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 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 112 HIS A 120 GLN C 90 GLN ** D 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5581 Z= 0.185 Angle : 0.541 8.105 7536 Z= 0.281 Chirality : 0.043 0.199 882 Planarity : 0.004 0.059 957 Dihedral : 5.340 54.335 734 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.86 % Allowed : 31.28 % Favored : 63.86 % 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: -0.20 (0.34), residues: 665 helix: 0.87 (0.31), residues: 301 sheet: -2.35 (0.49), residues: 98 loop : -0.22 (0.41), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 68 HIS 0.003 0.001 HIS A 56 PHE 0.020 0.001 PHE B 108 TYR 0.013 0.001 TYR A 88 ARG 0.008 0.000 ARG D 44 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 71 time to evaluate : 0.638 Fit side-chains REVERT: A 54 TYR cc_start: 0.6808 (t80) cc_final: 0.6573 (t80) REVERT: A 115 GLU cc_start: 0.6187 (OUTLIER) cc_final: 0.4274 (mp0) REVERT: C 30 MET cc_start: 0.5982 (OUTLIER) cc_final: 0.5365 (pmm) REVERT: C 56 LYS cc_start: 0.8440 (tmmt) cc_final: 0.8062 (tptp) REVERT: D 58 ARG cc_start: 0.7912 (ttp-110) cc_final: 0.7251 (mtm-85) REVERT: D 82 HIS cc_start: 0.5407 (OUTLIER) cc_final: 0.4775 (t70) REVERT: D 213 ASP cc_start: 0.8184 (OUTLIER) cc_final: 0.7462 (t70) REVERT: D 347 LYS cc_start: 0.6187 (tptp) cc_final: 0.5403 (ttpt) outliers start: 30 outliers final: 23 residues processed: 94 average time/residue: 0.2319 time to fit residues: 27.3265 Evaluate side-chains 94 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 67 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 30 CYS Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 30 MET Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 82 HIS Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 193 ILE Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 284 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 14 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 39 optimal weight: 0.0870 chunk 61 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 112 HIS C 90 GLN ** D 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5188 r_free = 0.5188 target = 0.293857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4883 r_free = 0.4883 target = 0.249596 restraints weight = 4919.879| |-----------------------------------------------------------------------------| r_work (start): 0.4877 rms_B_bonded: 1.55 r_work: 0.4536 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.4536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5581 Z= 0.184 Angle : 0.557 8.489 7536 Z= 0.290 Chirality : 0.044 0.201 882 Planarity : 0.004 0.059 957 Dihedral : 5.303 52.310 734 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 4.38 % Allowed : 31.93 % Favored : 63.70 % 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: -0.18 (0.34), residues: 665 helix: 0.89 (0.31), residues: 301 sheet: -2.33 (0.49), residues: 98 loop : -0.22 (0.40), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 68 HIS 0.003 0.001 HIS A 112 PHE 0.020 0.001 PHE B 108 TYR 0.014 0.001 TYR A 88 ARG 0.009 0.000 ARG D 44 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1576.06 seconds wall clock time: 29 minutes 42.76 seconds (1782.76 seconds total)