Starting phenix.real_space_refine on Sun Mar 10 23:42:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vq7_32087/03_2024/7vq7_32087.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vq7_32087/03_2024/7vq7_32087.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vq7_32087/03_2024/7vq7_32087.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vq7_32087/03_2024/7vq7_32087.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vq7_32087/03_2024/7vq7_32087.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vq7_32087/03_2024/7vq7_32087.pdb" } resolution = 3.6 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= 0.006 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: 5 Type Number sf(0) Gaussians Al 1 5.89 5 S 34 5.16 5 C 3942 2.51 5 N 1030 2.21 5 O 1120 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 5": "NH1" <-> "NH2" Residue "A GLU 6": "OE1" <-> "OE2" Residue "A ARG 9": "NH1" <-> "NH2" Residue "A ARG 13": "NH1" <-> "NH2" Residue "A ARG 20": "NH1" <-> "NH2" Residue "A GLU 156": "OE1" <-> "OE2" Residue "A GLU 163": "OE1" <-> "OE2" Residue "A GLU 234": "OE1" <-> "OE2" Residue "A GLU 246": "OE1" <-> "OE2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 316": "OE1" <-> "OE2" Residue "A ARG 400": "NH1" <-> "NH2" Residue "B ARG 5": "NH1" <-> "NH2" Residue "B GLU 6": "OE1" <-> "OE2" Residue "B ARG 9": "NH1" <-> "NH2" Residue "B ARG 13": "NH1" <-> "NH2" Residue "B ARG 20": "NH1" <-> "NH2" Residue "B GLU 156": "OE1" <-> "OE2" Residue "B GLU 163": "OE1" <-> "OE2" Residue "B GLU 234": "OE1" <-> "OE2" Residue "B GLU 246": "OE1" <-> "OE2" Residue "B ARG 265": "NH1" <-> "NH2" Residue "B PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 316": "OE1" <-> "OE2" Residue "B ARG 400": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6127 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3063 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 10, 'TRANS': 378} Chain breaks: 2 Chain: "B" Number of atoms: 3063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3063 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 10, 'TRANS': 378} Chain breaks: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' AL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.17, per 1000 atoms: 0.68 Number of scatterers: 6127 At special positions: 0 Unit cell: (86.19, 84.162, 111.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 34 16.00 Al 1 13.00 O 1120 8.00 N 1030 7.00 C 3942 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 - 3.50 Amino acid : False - 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: 2.79 Conformation dependent library (CDL) restraints added in 1.8 seconds 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1468 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 0 sheets defined 86.0% alpha, 0.0% 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 1 through 18 removed outlier: 3.743A pdb=" N ARG A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASP A 18 " --> pdb=" O VAL A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 39 removed outlier: 3.728A pdb=" N GLY A 29 " --> pdb=" O ALA A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 66 removed outlier: 3.518A pdb=" N PHE A 66 " --> pdb=" O VAL A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 102 removed outlier: 3.966A pdb=" N GLY A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 125 Processing helix chain 'A' and resid 127 through 133 removed outlier: 3.876A pdb=" N LYS A 133 " --> pdb=" O TRP A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 150 Processing helix chain 'A' and resid 154 through 183 removed outlier: 3.766A pdb=" N ILE A 158 " --> pdb=" O ARG A 154 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N MET A 159 " --> pdb=" O ASP A 155 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A 183 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 214 Processing helix chain 'A' and resid 223 through 240 removed outlier: 5.001A pdb=" N ARG A 235 " --> pdb=" O LYS A 231 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N TYR A 236 " --> pdb=" O ASN A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 267 through 293 removed outlier: 3.611A pdb=" N TYR A 271 " --> pdb=" O PRO A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 304 removed outlier: 3.638A pdb=" N LYS A 303 " --> pdb=" O PRO A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 331 Processing helix chain 'A' and resid 335 through 356 removed outlier: 4.058A pdb=" N ILE A 339 " --> pdb=" O SER A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 399 Processing helix chain 'B' and resid 2 through 18 removed outlier: 3.811A pdb=" N ASP B 18 " --> pdb=" O VAL B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 39 removed outlier: 3.728A pdb=" N GLY B 29 " --> pdb=" O ALA B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 66 removed outlier: 3.518A pdb=" N PHE B 66 " --> pdb=" O VAL B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 102 removed outlier: 3.967A pdb=" N GLY B 102 " --> pdb=" O ALA B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 125 Processing helix chain 'B' and resid 127 through 133 removed outlier: 3.876A pdb=" N LYS B 133 " --> pdb=" O TRP B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 150 Processing helix chain 'B' and resid 154 through 183 removed outlier: 3.766A pdb=" N ILE B 158 " --> pdb=" O ARG B 154 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N MET B 159 " --> pdb=" O ASP B 155 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL B 183 " --> pdb=" O ILE B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 214 Processing helix chain 'B' and resid 223 through 240 removed outlier: 5.000A pdb=" N ARG B 235 " --> pdb=" O LYS B 231 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N TYR B 236 " --> pdb=" O ASN B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 254 Processing helix chain 'B' and resid 267 through 293 removed outlier: 3.610A pdb=" N TYR B 271 " --> pdb=" O PRO B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 304 removed outlier: 3.638A pdb=" N LYS B 303 " --> pdb=" O PRO B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 331 Processing helix chain 'B' and resid 335 through 356 removed outlier: 4.058A pdb=" N ILE B 339 " --> pdb=" O SER B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 399 514 hydrogen bonds defined for protein. 1542 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: 1.86 Time building geometry restraints manager: 2.80 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: 1960 1.34 - 1.46: 1387 1.46 - 1.58: 2833 1.58 - 1.70: 0 1.70 - 1.82: 60 Bond restraints: 6240 Sorted by residual: bond pdb=" N HIS A 266 " pdb=" CA HIS A 266 " ideal model delta sigma weight residual 1.458 1.437 0.022 1.25e-02 6.40e+03 2.97e+00 bond pdb=" N HIS B 266 " pdb=" CA HIS B 266 " ideal model delta sigma weight residual 1.458 1.438 0.021 1.25e-02 6.40e+03 2.71e+00 bond pdb=" C TRP A 255 " pdb=" N GLU A 256 " ideal model delta sigma weight residual 1.329 1.305 0.023 1.60e-02 3.91e+03 2.11e+00 bond pdb=" C TRP B 255 " pdb=" N GLU B 256 " ideal model delta sigma weight residual 1.329 1.306 0.023 1.60e-02 3.91e+03 2.03e+00 bond pdb=" CB THR A 73 " pdb=" CG2 THR A 73 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.90e+00 ... (remaining 6235 not shown) Histogram of bond angle deviations from ideal: 100.53 - 107.23: 157 107.23 - 113.93: 3675 113.93 - 120.62: 2873 120.62 - 127.32: 1667 127.32 - 134.01: 50 Bond angle restraints: 8422 Sorted by residual: angle pdb=" N HIS A 266 " pdb=" CA HIS A 266 " pdb=" C HIS A 266 " ideal model delta sigma weight residual 109.10 102.60 6.50 1.91e+00 2.74e-01 1.16e+01 angle pdb=" N HIS B 266 " pdb=" CA HIS B 266 " pdb=" C HIS B 266 " ideal model delta sigma weight residual 109.10 102.63 6.47 1.91e+00 2.74e-01 1.15e+01 angle pdb=" CA LYS B 3 " pdb=" CB LYS B 3 " pdb=" CG LYS B 3 " ideal model delta sigma weight residual 114.10 120.24 -6.14 2.00e+00 2.50e-01 9.41e+00 angle pdb=" CA LYS A 3 " pdb=" CB LYS A 3 " pdb=" CG LYS A 3 " ideal model delta sigma weight residual 114.10 120.23 -6.13 2.00e+00 2.50e-01 9.38e+00 angle pdb=" C PHE B 134 " pdb=" CA PHE B 134 " pdb=" CB PHE B 134 " ideal model delta sigma weight residual 111.13 107.09 4.04 1.61e+00 3.86e-01 6.29e+00 ... (remaining 8417 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.55: 3200 16.55 - 33.10: 396 33.10 - 49.65: 112 49.65 - 66.21: 38 66.21 - 82.76: 10 Dihedral angle restraints: 3756 sinusoidal: 1494 harmonic: 2262 Sorted by residual: dihedral pdb=" CA LEU B 233 " pdb=" C LEU B 233 " pdb=" N GLU B 234 " pdb=" CA GLU B 234 " ideal model delta harmonic sigma weight residual -180.00 -158.86 -21.14 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA LEU A 233 " pdb=" C LEU A 233 " pdb=" N GLU A 234 " pdb=" CA GLU A 234 " ideal model delta harmonic sigma weight residual -180.00 -158.94 -21.06 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA ILE B 181 " pdb=" C ILE B 181 " pdb=" N PHE B 182 " pdb=" CA PHE B 182 " ideal model delta harmonic sigma weight residual -180.00 -161.63 -18.37 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 3753 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 412 0.027 - 0.055: 411 0.055 - 0.082: 98 0.082 - 0.109: 40 0.109 - 0.136: 13 Chirality restraints: 974 Sorted by residual: chirality pdb=" CA PRO B 365 " pdb=" N PRO B 365 " pdb=" C PRO B 365 " pdb=" CB PRO B 365 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.65e-01 chirality pdb=" CA PRO A 365 " pdb=" N PRO A 365 " pdb=" C PRO A 365 " pdb=" CB PRO A 365 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.13 2.00e-01 2.50e+01 4.45e-01 chirality pdb=" CA ILE B 298 " pdb=" N ILE B 298 " pdb=" C ILE B 298 " pdb=" CB ILE B 298 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.30e-01 ... (remaining 971 not shown) Planarity restraints: 1052 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS B 184 " -0.023 5.00e-02 4.00e+02 3.57e-02 2.04e+00 pdb=" N PRO B 185 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO B 185 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 185 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 184 " -0.023 5.00e-02 4.00e+02 3.54e-02 2.01e+00 pdb=" N PRO A 185 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 185 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 185 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 364 " -0.021 5.00e-02 4.00e+02 3.11e-02 1.55e+00 pdb=" N PRO A 365 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 365 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 365 " -0.017 5.00e-02 4.00e+02 ... (remaining 1049 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 68 2.64 - 3.20: 5998 3.20 - 3.77: 9393 3.77 - 4.33: 12175 4.33 - 4.90: 20108 Nonbonded interactions: 47742 Sorted by model distance: nonbonded pdb=" SD MET B 60 " pdb="AL AL A 601 " model vdw 2.070 2.380 nonbonded pdb=" O CYS A 176 " pdb=" OG SER A 180 " model vdw 2.198 2.440 nonbonded pdb=" O SER A 294 " pdb=" NE2 GLN A 297 " model vdw 2.217 2.520 nonbonded pdb=" O SER B 294 " pdb=" NE2 GLN B 297 " model vdw 2.217 2.520 nonbonded pdb=" O LYS B 228 " pdb=" ND2 ASN B 232 " model vdw 2.255 2.520 ... (remaining 47737 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 405) selection = chain 'B' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 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: 1.540 Check model and map are aligned: 0.190 Set scattering table: 0.000 Process input model: 22.050 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 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 : 0.007 0.046 6240 Z= 0.480 Angle : 0.755 6.503 8422 Z= 0.452 Chirality : 0.042 0.136 974 Planarity : 0.004 0.036 1052 Dihedral : 16.807 82.757 2288 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 4.87 % Allowed : 7.82 % Favored : 87.32 % 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: -1.30 (0.27), residues: 766 helix: -0.48 (0.18), residues: 638 sheet: None (None), residues: 0 loop : -2.07 (0.57), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 255 HIS 0.004 0.002 HIS A 259 PHE 0.017 0.002 PHE B 206 TYR 0.011 0.002 TYR B 291 ARG 0.004 0.000 ARG B 9 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 147 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 ARG cc_start: 0.6940 (mtt-85) cc_final: 0.6086 (ttm110) REVERT: A 230 LYS cc_start: 0.7448 (mmtt) cc_final: 0.7110 (tptp) REVERT: A 265 ARG cc_start: 0.7029 (mmt180) cc_final: 0.6633 (tpp-160) REVERT: A 304 LYS cc_start: 0.7320 (OUTLIER) cc_final: 0.6693 (ttpt) REVERT: A 321 MET cc_start: 0.8308 (mtt) cc_final: 0.8093 (mtt) REVERT: A 331 MET cc_start: 0.5936 (mtm) cc_final: 0.5244 (mpp) REVERT: B 265 ARG cc_start: 0.6818 (mmt180) cc_final: 0.6558 (tpp-160) REVERT: B 321 MET cc_start: 0.8252 (mtt) cc_final: 0.8001 (mtt) REVERT: B 331 MET cc_start: 0.6491 (mtm) cc_final: 0.5717 (mpp) outliers start: 33 outliers final: 6 residues processed: 167 average time/residue: 0.2002 time to fit residues: 42.7846 Evaluate side-chains 121 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 114 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 363 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 38 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 69 optimal weight: 0.1980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 HIS A 261 GLN A 289 ASN A 319 ASN B 193 HIS B 232 ASN B 261 GLN B 289 ASN B 293 ASN B 319 ASN B 330 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6240 Z= 0.169 Angle : 0.475 5.477 8422 Z= 0.255 Chirality : 0.036 0.143 974 Planarity : 0.003 0.034 1052 Dihedral : 5.574 52.766 842 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.83 % Allowed : 15.04 % Favored : 81.12 % 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: 1.66 (0.30), residues: 766 helix: 1.52 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -1.39 (0.64), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 255 HIS 0.003 0.001 HIS B 205 PHE 0.023 0.001 PHE B 38 TYR 0.016 0.001 TYR B 40 ARG 0.004 0.000 ARG A 311 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 134 time to evaluate : 0.677 Fit side-chains REVERT: A 3 LYS cc_start: 0.6196 (pptt) cc_final: 0.5403 (pptt) REVERT: A 5 ARG cc_start: 0.6982 (mtt-85) cc_final: 0.6226 (ttm110) REVERT: A 230 LYS cc_start: 0.7332 (mmtt) cc_final: 0.7013 (tptp) REVERT: A 265 ARG cc_start: 0.6944 (mmt180) cc_final: 0.6725 (tpp-160) REVERT: A 331 MET cc_start: 0.5899 (mtm) cc_final: 0.5232 (mpp) REVERT: B 331 MET cc_start: 0.6275 (mtm) cc_final: 0.5540 (mpp) outliers start: 26 outliers final: 15 residues processed: 151 average time/residue: 0.1836 time to fit residues: 36.0183 Evaluate side-chains 127 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 112 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 TYR Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 363 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 9.9990 chunk 21 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 69 optimal weight: 9.9990 chunk 74 optimal weight: 7.9990 chunk 61 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 232 ASN A 261 GLN A 393 HIS B 79 ASN B 261 GLN B 393 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 6240 Z= 0.330 Angle : 0.550 5.619 8422 Z= 0.296 Chirality : 0.039 0.150 974 Planarity : 0.004 0.038 1052 Dihedral : 4.878 46.985 836 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 4.57 % Allowed : 19.32 % Favored : 76.11 % 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: 2.27 (0.31), residues: 766 helix: 2.01 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -1.33 (0.60), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 255 HIS 0.003 0.001 HIS B 259 PHE 0.020 0.002 PHE B 206 TYR 0.020 0.002 TYR B 40 ARG 0.004 0.000 ARG A 311 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 119 time to evaluate : 0.752 Fit side-chains revert: symmetry clash REVERT: A 5 ARG cc_start: 0.7367 (mtt-85) cc_final: 0.6504 (ttm110) REVERT: A 56 MET cc_start: 0.7574 (ptp) cc_final: 0.7374 (ptp) REVERT: A 265 ARG cc_start: 0.7010 (mmt180) cc_final: 0.6690 (tpp-160) REVERT: A 270 GLN cc_start: 0.7955 (mt0) cc_final: 0.7704 (mp10) REVERT: A 321 MET cc_start: 0.8275 (mtt) cc_final: 0.7830 (mtt) REVERT: B 270 GLN cc_start: 0.8001 (mt0) cc_final: 0.7776 (mp10) REVERT: B 321 MET cc_start: 0.8178 (mtt) cc_final: 0.7716 (mtt) REVERT: B 331 MET cc_start: 0.6202 (mtm) cc_final: 0.5629 (mpp) REVERT: B 405 MET cc_start: 0.3882 (ttm) cc_final: 0.2192 (mpp) outliers start: 31 outliers final: 21 residues processed: 142 average time/residue: 0.1780 time to fit residues: 33.3902 Evaluate side-chains 134 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 113 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 39 TYR Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 261 GLN Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 363 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 46 optimal weight: 8.9990 chunk 69 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 65 optimal weight: 8.9990 chunk 19 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6240 Z= 0.181 Angle : 0.471 5.729 8422 Z= 0.254 Chirality : 0.036 0.151 974 Planarity : 0.003 0.038 1052 Dihedral : 4.363 40.311 835 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.98 % Allowed : 21.98 % Favored : 74.04 % 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: 2.96 (0.31), residues: 766 helix: 2.44 (0.20), residues: 648 sheet: None (None), residues: 0 loop : -0.90 (0.64), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 255 HIS 0.003 0.001 HIS B 205 PHE 0.016 0.001 PHE B 206 TYR 0.020 0.002 TYR B 40 ARG 0.002 0.000 ARG A 311 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 121 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 ARG cc_start: 0.7352 (mtt-85) cc_final: 0.6493 (ttm110) REVERT: A 56 MET cc_start: 0.7585 (ptp) cc_final: 0.7343 (ptp) REVERT: A 265 ARG cc_start: 0.7000 (mmt180) cc_final: 0.6799 (tpp-160) REVERT: A 321 MET cc_start: 0.8030 (mtt) cc_final: 0.7489 (mtt) REVERT: A 331 MET cc_start: 0.5790 (mpp) cc_final: 0.4975 (mpp) REVERT: B 3 LYS cc_start: 0.6761 (pptt) cc_final: 0.6502 (pptt) REVERT: B 244 SER cc_start: 0.8719 (OUTLIER) cc_final: 0.8105 (t) REVERT: B 321 MET cc_start: 0.8039 (mtt) cc_final: 0.7586 (mtt) REVERT: B 331 MET cc_start: 0.6127 (mtm) cc_final: 0.5400 (mpp) outliers start: 27 outliers final: 18 residues processed: 140 average time/residue: 0.1870 time to fit residues: 34.1732 Evaluate side-chains 133 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 114 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 TYR Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 363 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 30 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 chunk 65 optimal weight: 0.4980 chunk 18 optimal weight: 0.8980 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN B 261 GLN B 293 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6240 Z= 0.205 Angle : 0.476 6.640 8422 Z= 0.253 Chirality : 0.037 0.146 974 Planarity : 0.003 0.033 1052 Dihedral : 4.106 34.302 835 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 4.57 % Allowed : 24.34 % Favored : 71.09 % 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: 3.26 (0.31), residues: 766 helix: 2.71 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -0.83 (0.62), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 255 HIS 0.002 0.001 HIS B 259 PHE 0.022 0.001 PHE B 38 TYR 0.035 0.002 TYR B 291 ARG 0.003 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 119 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 ARG cc_start: 0.7458 (mtt-85) cc_final: 0.6295 (ttm110) REVERT: A 56 MET cc_start: 0.7620 (ptp) cc_final: 0.7379 (ptp) REVERT: A 321 MET cc_start: 0.7939 (mtt) cc_final: 0.7415 (mtt) REVERT: A 331 MET cc_start: 0.5797 (mpp) cc_final: 0.5209 (mpp) REVERT: A 405 MET cc_start: 0.2612 (OUTLIER) cc_final: 0.2349 (mmm) REVERT: B 3 LYS cc_start: 0.6761 (pptt) cc_final: 0.6297 (pptt) REVERT: B 244 SER cc_start: 0.8742 (OUTLIER) cc_final: 0.8180 (t) REVERT: B 293 ASN cc_start: 0.8719 (OUTLIER) cc_final: 0.8429 (t0) REVERT: B 321 MET cc_start: 0.8053 (mtt) cc_final: 0.7556 (mtt) REVERT: B 331 MET cc_start: 0.5981 (mtm) cc_final: 0.5375 (mpp) outliers start: 31 outliers final: 15 residues processed: 139 average time/residue: 0.1869 time to fit residues: 33.7171 Evaluate side-chains 131 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 113 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 TYR Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 405 MET Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain B residue 315 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 24 optimal weight: 0.7980 chunk 66 optimal weight: 8.9990 chunk 14 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 6 optimal weight: 0.8980 chunk 38 optimal weight: 0.2980 chunk 70 optimal weight: 9.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN A 393 HIS B 261 GLN B 293 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6240 Z= 0.163 Angle : 0.471 8.728 8422 Z= 0.246 Chirality : 0.036 0.145 974 Planarity : 0.003 0.033 1052 Dihedral : 3.833 24.502 833 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.54 % Allowed : 25.66 % Favored : 70.80 % 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: 3.47 (0.31), residues: 766 helix: 2.76 (0.20), residues: 648 sheet: None (None), residues: 0 loop : -0.55 (0.66), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 255 HIS 0.002 0.001 HIS B 205 PHE 0.011 0.001 PHE B 215 TYR 0.027 0.002 TYR B 291 ARG 0.003 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 125 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 ARG cc_start: 0.7403 (mtt-85) cc_final: 0.6354 (ttm110) REVERT: A 56 MET cc_start: 0.7578 (ptp) cc_final: 0.7359 (ptp) REVERT: A 155 ASP cc_start: 0.6192 (OUTLIER) cc_final: 0.5956 (m-30) REVERT: A 265 ARG cc_start: 0.6951 (tpp-160) cc_final: 0.6681 (tpp-160) REVERT: A 321 MET cc_start: 0.7742 (mtt) cc_final: 0.7202 (mtt) REVERT: A 331 MET cc_start: 0.5714 (mpp) cc_final: 0.5109 (mpp) REVERT: A 377 MET cc_start: 0.7048 (mmt) cc_final: 0.6804 (mtt) REVERT: A 405 MET cc_start: 0.2529 (OUTLIER) cc_final: 0.2229 (mmm) REVERT: B 3 LYS cc_start: 0.6439 (pptt) cc_final: 0.6055 (pptt) REVERT: B 74 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8710 (tt) REVERT: B 209 ASP cc_start: 0.8393 (m-30) cc_final: 0.8188 (m-30) REVERT: B 244 SER cc_start: 0.8725 (OUTLIER) cc_final: 0.8161 (t) REVERT: B 293 ASN cc_start: 0.8457 (OUTLIER) cc_final: 0.8142 (t0) REVERT: B 331 MET cc_start: 0.6031 (mtm) cc_final: 0.5420 (mpp) outliers start: 24 outliers final: 13 residues processed: 141 average time/residue: 0.1789 time to fit residues: 33.4297 Evaluate side-chains 131 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 113 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ARG Chi-restraints excluded: chain A residue 39 TYR Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 405 MET Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain B residue 315 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 33 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 22 optimal weight: 0.1980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN B 261 GLN B 293 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6240 Z= 0.170 Angle : 0.485 9.570 8422 Z= 0.252 Chirality : 0.036 0.152 974 Planarity : 0.003 0.033 1052 Dihedral : 3.758 16.803 833 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.69 % Allowed : 26.99 % Favored : 69.32 % 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: 3.56 (0.31), residues: 766 helix: 2.80 (0.20), residues: 648 sheet: None (None), residues: 0 loop : -0.34 (0.66), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 255 HIS 0.002 0.001 HIS B 205 PHE 0.018 0.001 PHE B 38 TYR 0.013 0.001 TYR A 40 ARG 0.002 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 116 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 ARG cc_start: 0.7462 (mtt-85) cc_final: 0.6372 (ttm110) REVERT: A 56 MET cc_start: 0.7561 (ptp) cc_final: 0.7341 (ptp) REVERT: A 155 ASP cc_start: 0.6216 (OUTLIER) cc_final: 0.5980 (m-30) REVERT: A 321 MET cc_start: 0.7752 (mtt) cc_final: 0.7181 (mtt) REVERT: A 331 MET cc_start: 0.5774 (mpp) cc_final: 0.5118 (mpp) REVERT: A 405 MET cc_start: 0.2630 (OUTLIER) cc_final: 0.2263 (mmm) REVERT: B 74 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8717 (tt) REVERT: B 244 SER cc_start: 0.8718 (OUTLIER) cc_final: 0.8164 (t) REVERT: B 293 ASN cc_start: 0.8273 (OUTLIER) cc_final: 0.7985 (t0) REVERT: B 321 MET cc_start: 0.7817 (mtt) cc_final: 0.7186 (mtt) REVERT: B 331 MET cc_start: 0.6024 (mtm) cc_final: 0.5316 (mpp) outliers start: 25 outliers final: 15 residues processed: 133 average time/residue: 0.1772 time to fit residues: 31.0705 Evaluate side-chains 128 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 108 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 TYR Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 405 MET Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain B residue 315 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 0.0030 chunk 46 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 6 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 66 optimal weight: 9.9990 chunk 70 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 overall best weight: 1.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN A 393 HIS B 261 GLN B 293 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6240 Z= 0.223 Angle : 0.531 11.784 8422 Z= 0.274 Chirality : 0.038 0.156 974 Planarity : 0.003 0.032 1052 Dihedral : 3.813 17.602 832 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.83 % Allowed : 26.11 % Favored : 70.06 % 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: 3.53 (0.31), residues: 766 helix: 2.85 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -0.48 (0.61), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 255 HIS 0.002 0.001 HIS B 205 PHE 0.010 0.001 PHE B 206 TYR 0.023 0.002 TYR B 40 ARG 0.002 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 108 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 ARG cc_start: 0.7606 (mtt-85) cc_final: 0.6510 (ttm110) REVERT: A 56 MET cc_start: 0.7557 (ptp) cc_final: 0.7337 (ptp) REVERT: A 155 ASP cc_start: 0.6319 (OUTLIER) cc_final: 0.6092 (m-30) REVERT: A 321 MET cc_start: 0.7817 (mtt) cc_final: 0.7271 (mtt) REVERT: A 331 MET cc_start: 0.5846 (mpp) cc_final: 0.5176 (mpp) REVERT: A 405 MET cc_start: 0.2824 (mpp) cc_final: 0.2424 (mmm) REVERT: B 74 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8754 (tt) REVERT: B 244 SER cc_start: 0.8748 (OUTLIER) cc_final: 0.8200 (t) REVERT: B 293 ASN cc_start: 0.8283 (OUTLIER) cc_final: 0.7974 (t0) REVERT: B 311 ARG cc_start: 0.8097 (ttm110) cc_final: 0.7884 (mtt180) REVERT: B 321 MET cc_start: 0.7890 (mtt) cc_final: 0.7137 (mtt) REVERT: B 331 MET cc_start: 0.6077 (mtm) cc_final: 0.5350 (mpp) outliers start: 26 outliers final: 17 residues processed: 127 average time/residue: 0.1934 time to fit residues: 31.9652 Evaluate side-chains 128 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 107 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 TYR Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain B residue 315 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 61 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 50 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN B 261 GLN B 293 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6240 Z= 0.206 Angle : 0.523 12.128 8422 Z= 0.269 Chirality : 0.037 0.152 974 Planarity : 0.003 0.032 1052 Dihedral : 3.779 17.730 832 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.54 % Allowed : 26.70 % Favored : 69.76 % 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: 3.59 (0.31), residues: 766 helix: 2.81 (0.20), residues: 648 sheet: None (None), residues: 0 loop : -0.32 (0.65), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 255 HIS 0.002 0.001 HIS B 205 PHE 0.009 0.001 PHE B 206 TYR 0.022 0.002 TYR B 40 ARG 0.002 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 109 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 ARG cc_start: 0.7662 (mtt-85) cc_final: 0.6398 (ttm110) REVERT: A 56 MET cc_start: 0.7554 (ptp) cc_final: 0.7330 (ptp) REVERT: A 155 ASP cc_start: 0.6328 (OUTLIER) cc_final: 0.6093 (m-30) REVERT: A 321 MET cc_start: 0.7819 (mtt) cc_final: 0.7243 (mtt) REVERT: A 331 MET cc_start: 0.6012 (mpp) cc_final: 0.5355 (mpp) REVERT: A 405 MET cc_start: 0.2995 (mpp) cc_final: 0.2564 (mmm) REVERT: B 74 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8684 (tt) REVERT: B 244 SER cc_start: 0.8755 (OUTLIER) cc_final: 0.8183 (t) REVERT: B 293 ASN cc_start: 0.8359 (OUTLIER) cc_final: 0.8041 (t0) REVERT: B 321 MET cc_start: 0.7882 (mtt) cc_final: 0.7116 (mtt) REVERT: B 331 MET cc_start: 0.6135 (mtm) cc_final: 0.5377 (mpp) outliers start: 24 outliers final: 16 residues processed: 126 average time/residue: 0.1683 time to fit residues: 28.2044 Evaluate side-chains 126 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 106 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 TYR Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain B residue 315 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 3.9990 chunk 60 optimal weight: 0.2980 chunk 6 optimal weight: 5.9990 chunk 46 optimal weight: 8.9990 chunk 36 optimal weight: 0.6980 chunk 47 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 8 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN B 261 GLN B 293 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6240 Z= 0.186 Angle : 0.544 15.438 8422 Z= 0.276 Chirality : 0.037 0.201 974 Planarity : 0.003 0.031 1052 Dihedral : 3.742 17.452 832 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.54 % Allowed : 26.99 % Favored : 69.47 % 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: 3.67 (0.31), residues: 766 helix: 2.88 (0.20), residues: 648 sheet: None (None), residues: 0 loop : -0.37 (0.64), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 255 HIS 0.002 0.001 HIS B 205 PHE 0.009 0.001 PHE B 206 TYR 0.022 0.001 TYR B 40 ARG 0.002 0.000 ARG A 20 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 112 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 ARG cc_start: 0.7670 (mtt-85) cc_final: 0.7006 (ttm170) REVERT: A 56 MET cc_start: 0.7514 (ptp) cc_final: 0.7308 (ptp) REVERT: A 155 ASP cc_start: 0.6324 (OUTLIER) cc_final: 0.6082 (m-30) REVERT: A 321 MET cc_start: 0.7861 (mtt) cc_final: 0.7276 (mtt) REVERT: A 331 MET cc_start: 0.6034 (mpp) cc_final: 0.5400 (mpp) REVERT: A 405 MET cc_start: 0.2878 (mpp) cc_final: 0.2570 (mmm) REVERT: B 74 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8721 (tt) REVERT: B 244 SER cc_start: 0.8740 (OUTLIER) cc_final: 0.8184 (t) REVERT: B 321 MET cc_start: 0.7854 (mtt) cc_final: 0.7101 (mtt) REVERT: B 331 MET cc_start: 0.6300 (mtm) cc_final: 0.5342 (mpp) outliers start: 24 outliers final: 16 residues processed: 129 average time/residue: 0.1702 time to fit residues: 29.3883 Evaluate side-chains 129 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 110 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 39 TYR Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 315 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 60 optimal weight: 0.3980 chunk 25 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 43 optimal weight: 0.5980 chunk 69 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN B 261 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.172462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.127533 restraints weight = 7981.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.130921 restraints weight = 5176.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.133057 restraints weight = 4061.363| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.4406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6240 Z= 0.194 Angle : 0.539 14.741 8422 Z= 0.280 Chirality : 0.038 0.229 974 Planarity : 0.003 0.031 1052 Dihedral : 3.779 17.765 832 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.10 % Allowed : 27.58 % Favored : 69.32 % 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: 3.68 (0.31), residues: 766 helix: 2.90 (0.20), residues: 648 sheet: None (None), residues: 0 loop : -0.49 (0.63), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 255 HIS 0.002 0.001 HIS A 205 PHE 0.009 0.001 PHE B 206 TYR 0.022 0.002 TYR B 40 ARG 0.002 0.000 ARG A 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1402.41 seconds wall clock time: 26 minutes 36.87 seconds (1596.87 seconds total)