Starting phenix.real_space_refine on Mon Jun 24 19:54:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vzn_43683/06_2024/8vzn_43683_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vzn_43683/06_2024/8vzn_43683.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vzn_43683/06_2024/8vzn_43683.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vzn_43683/06_2024/8vzn_43683.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vzn_43683/06_2024/8vzn_43683_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vzn_43683/06_2024/8vzn_43683_updated.pdb" } resolution = 2.77 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= 0.033 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 26 5.16 5 C 3068 2.51 5 N 748 2.21 5 O 814 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 267": "OE1" <-> "OE2" Residue "A PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 356": "NH1" <-> "NH2" Residue "A GLU 365": "OE1" <-> "OE2" Residue "A PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 399": "OE1" <-> "OE2" Residue "A TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 70": "NH1" <-> "NH2" Residue "B ARG 90": "NH1" <-> "NH2" Residue "B TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 101": "NH1" <-> "NH2" Residue "B TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 119": "OD1" <-> "OD2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 4656 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3246 Classifications: {'peptide': 417} Link IDs: {'PTRANS': 15, 'TRANS': 401} Chain breaks: 1 Chain: "B" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 933 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "C" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 470 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 3, 'TRANS': 58} Chain breaks: 1 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'CHT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.92, per 1000 atoms: 0.84 Number of scatterers: 4656 At special positions: 0 Unit cell: (73.87, 68.06, 118.69, 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 26 16.00 O 814 8.00 N 748 7.00 C 3068 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS B 99 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 89 " distance=2.05 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: 1.91 Conformation dependent library (CDL) restraints added in 874.3 milliseconds 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1090 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 18 helices and 3 sheets defined 56.5% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 106 through 126 removed outlier: 3.504A pdb=" N VAL A 111 " --> pdb=" O ARG A 107 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 138 Processing helix chain 'A' and resid 143 through 170 removed outlier: 3.911A pdb=" N LEU A 149 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N SER A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N TYR A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N MET A 154 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE A 158 " --> pdb=" O MET A 154 " (cutoff:3.500A) Proline residue: A 159 - end of helix removed outlier: 5.265A pdb=" N LEU A 162 " --> pdb=" O ILE A 158 " (cutoff:3.500A) Proline residue: A 163 - end of helix Processing helix chain 'A' and resid 173 through 194 removed outlier: 4.141A pdb=" N LEU A 192 " --> pdb=" O ALA A 188 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLY A 193 " --> pdb=" O TRP A 189 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N SER A 194 " --> pdb=" O VAL A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 218 removed outlier: 3.503A pdb=" N VAL A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE A 216 " --> pdb=" O VAL A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 228 Processing helix chain 'A' and resid 234 through 259 removed outlier: 3.913A pdb=" N ASN A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) Proline residue: A 256 - end of helix Processing helix chain 'A' and resid 269 through 294 removed outlier: 3.588A pdb=" N MET A 276 " --> pdb=" O HIS A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 311 Processing helix chain 'A' and resid 321 through 327 removed outlier: 3.630A pdb=" N ARG A 326 " --> pdb=" O SER A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 Processing helix chain 'A' and resid 354 through 361 Processing helix chain 'A' and resid 366 through 394 Processing helix chain 'A' and resid 397 through 418 Processing helix chain 'A' and resid 424 through 453 removed outlier: 4.010A pdb=" N LEU A 442 " --> pdb=" O MET A 438 " (cutoff:3.500A) Proline residue: A 443 - end of helix Processing helix chain 'A' and resid 458 through 487 Processing helix chain 'A' and resid 489 through 507 removed outlier: 3.981A pdb=" N LEU A 496 " --> pdb=" O GLY A 492 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE A 499 " --> pdb=" O PHE A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 520 Processing sheet with id= A, first strand: chain 'B' and resid 22 through 26 removed outlier: 3.557A pdb=" N THR B 81 " --> pdb=" O ASP B 76 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 125 through 127 removed outlier: 5.984A pdb=" N ARG B 41 " --> pdb=" O TRP B 50 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N TRP B 50 " --> pdb=" O ARG B 41 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ALA B 43 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LEU B 48 " --> pdb=" O ALA B 43 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 86 through 91 removed outlier: 6.101A pdb=" N GLN C 38 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N LEU C 47 " --> pdb=" O GLN C 38 " (cutoff:3.500A) 269 hydrogen bonds defined for protein. 795 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: 1.31 Time building geometry restraints manager: 2.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 690 1.29 - 1.42: 1370 1.42 - 1.55: 2680 1.55 - 1.68: 1 1.68 - 1.81: 41 Bond restraints: 4782 Sorted by residual: bond pdb=" CA TYR A 271 " pdb=" C TYR A 271 " ideal model delta sigma weight residual 1.524 1.432 0.092 1.32e-02 5.74e+03 4.81e+01 bond pdb=" CA ALA A 270 " pdb=" CB ALA A 270 " ideal model delta sigma weight residual 1.529 1.424 0.105 1.78e-02 3.16e+03 3.50e+01 bond pdb=" C ARG A 106 " pdb=" O ARG A 106 " ideal model delta sigma weight residual 1.236 1.163 0.073 1.29e-02 6.01e+03 3.18e+01 bond pdb=" C ILE A 126 " pdb=" O ILE A 126 " ideal model delta sigma weight residual 1.235 1.155 0.080 1.45e-02 4.76e+03 3.04e+01 bond pdb=" C LYS B 102 " pdb=" O LYS B 102 " ideal model delta sigma weight residual 1.234 1.168 0.067 1.22e-02 6.72e+03 3.00e+01 ... (remaining 4777 not shown) Histogram of bond angle deviations from ideal: 97.00 - 104.54: 101 104.54 - 112.08: 2222 112.08 - 119.62: 1858 119.62 - 127.16: 2262 127.16 - 134.69: 63 Bond angle restraints: 6506 Sorted by residual: angle pdb=" O CYS A 120 " pdb=" C CYS A 120 " pdb=" N ASN A 121 " ideal model delta sigma weight residual 122.12 114.16 7.96 1.06e+00 8.90e-01 5.64e+01 angle pdb=" N ALA C 33 " pdb=" CA ALA C 33 " pdb=" C ALA C 33 " ideal model delta sigma weight residual 110.88 101.31 9.57 1.28e+00 6.10e-01 5.59e+01 angle pdb=" C GLN B 16 " pdb=" CA GLN B 16 " pdb=" CB GLN B 16 " ideal model delta sigma weight residual 108.68 118.86 -10.18 1.39e+00 5.18e-01 5.36e+01 angle pdb=" CA TRP A 425 " pdb=" C TRP A 425 " pdb=" O TRP A 425 " ideal model delta sigma weight residual 120.24 112.37 7.87 1.11e+00 8.12e-01 5.03e+01 angle pdb=" N TYR A 454 " pdb=" CA TYR A 454 " pdb=" CB TYR A 454 " ideal model delta sigma weight residual 110.42 118.54 -8.12 1.18e+00 7.18e-01 4.74e+01 ... (remaining 6501 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 2475 17.85 - 35.70: 210 35.70 - 53.55: 35 53.55 - 71.41: 13 71.41 - 89.26: 8 Dihedral angle restraints: 2741 sinusoidal: 1026 harmonic: 1715 Sorted by residual: dihedral pdb=" CD ARG B 70 " pdb=" NE ARG B 70 " pdb=" CZ ARG B 70 " pdb=" NH1 ARG B 70 " ideal model delta sinusoidal sigma weight residual 0.00 88.68 -88.68 1 1.00e+01 1.00e-02 9.38e+01 dihedral pdb=" CD ARG B 114 " pdb=" NE ARG B 114 " pdb=" CZ ARG B 114 " pdb=" NH1 ARG B 114 " ideal model delta sinusoidal sigma weight residual 0.00 87.99 -87.99 1 1.00e+01 1.00e-02 9.26e+01 dihedral pdb=" CD ARG A 107 " pdb=" NE ARG A 107 " pdb=" CZ ARG A 107 " pdb=" NH1 ARG A 107 " ideal model delta sinusoidal sigma weight residual 0.00 86.98 -86.98 1 1.00e+01 1.00e-02 9.09e+01 ... (remaining 2738 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 459 0.067 - 0.134: 198 0.134 - 0.201: 59 0.201 - 0.268: 17 0.268 - 0.335: 3 Chirality restraints: 736 Sorted by residual: chirality pdb=" CB VAL C 34 " pdb=" CA VAL C 34 " pdb=" CG1 VAL C 34 " pdb=" CG2 VAL C 34 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" CA SER A 104 " pdb=" N SER A 104 " pdb=" C SER A 104 " pdb=" CB SER A 104 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CA LYS C 40 " pdb=" N LYS C 40 " pdb=" C LYS C 40 " pdb=" CB LYS C 40 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 733 not shown) Planarity restraints: 795 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 70 " 1.103 9.50e-02 1.11e+02 4.94e-01 1.47e+02 pdb=" NE ARG B 70 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG B 70 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG B 70 " 0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG B 70 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 107 " -1.098 9.50e-02 1.11e+02 4.92e-01 1.46e+02 pdb=" NE ARG A 107 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG A 107 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 107 " -0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG A 107 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 114 " 1.089 9.50e-02 1.11e+02 4.88e-01 1.44e+02 pdb=" NE ARG B 114 " -0.067 2.00e-02 2.50e+03 pdb=" CZ ARG B 114 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG B 114 " 0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG B 114 " 0.015 2.00e-02 2.50e+03 ... (remaining 792 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 1650 2.84 - 3.36: 4398 3.36 - 3.87: 8175 3.87 - 4.39: 9892 4.39 - 4.90: 16088 Nonbonded interactions: 40203 Sorted by model distance: nonbonded pdb=" O LEU A 195 " pdb=" OH TYR B 104 " model vdw 2.330 2.440 nonbonded pdb=" O THR A 175 " pdb=" OG1 THR A 179 " model vdw 2.335 2.440 nonbonded pdb=" OH TYR A 128 " pdb=" OG1 THR A 203 " model vdw 2.369 2.440 nonbonded pdb=" O ALA A 449 " pdb=" OG1 THR A 453 " model vdw 2.379 2.440 nonbonded pdb=" N LYS B 102 " pdb=" O LYS B 102 " model vdw 2.414 2.496 ... (remaining 40198 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 11.370 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 19.070 Find NCS groups from input model: 0.130 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:12.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 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 : 0.015 0.105 4782 Z= 0.966 Angle : 1.531 10.176 6506 Z= 1.057 Chirality : 0.084 0.335 736 Planarity : 0.039 0.494 795 Dihedral : 15.045 89.256 1645 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.81 % Allowed : 8.82 % Favored : 88.38 % 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: -3.34 (0.29), residues: 586 helix: -1.97 (0.23), residues: 348 sheet: -2.12 (0.55), residues: 67 loop : -2.28 (0.42), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 121 HIS 0.008 0.003 HIS B 112 PHE 0.026 0.004 PHE A 436 TYR 0.019 0.003 TYR A 117 ARG 0.008 0.001 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 74 time to evaluate : 0.529 Fit side-chains REVERT: A 102 LYS cc_start: 0.6915 (tttm) cc_final: 0.6684 (ttmm) REVERT: A 253 PHE cc_start: 0.9205 (OUTLIER) cc_final: 0.7334 (t80) REVERT: A 381 MET cc_start: 0.8352 (mtm) cc_final: 0.8152 (mtp) REVERT: A 511 LYS cc_start: 0.8079 (tttt) cc_final: 0.7517 (mttp) REVERT: B 106 TRP cc_start: 0.8598 (OUTLIER) cc_final: 0.8396 (t-100) outliers start: 14 outliers final: 1 residues processed: 87 average time/residue: 1.3509 time to fit residues: 121.6941 Evaluate side-chains 64 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 61 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 PHE Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain B residue 106 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 ASN A 343 ASN A 422 ASN C 28 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4782 Z= 0.217 Angle : 0.562 7.368 6506 Z= 0.302 Chirality : 0.040 0.157 736 Planarity : 0.005 0.054 795 Dihedral : 5.944 54.012 651 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.80 % Allowed : 13.63 % Favored : 84.57 % 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: -0.63 (0.33), residues: 586 helix: 0.39 (0.27), residues: 348 sheet: -1.23 (0.59), residues: 65 loop : -1.57 (0.44), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 148 HIS 0.002 0.001 HIS B 38 PHE 0.018 0.002 PHE A 144 TYR 0.025 0.002 TYR A 117 ARG 0.007 0.001 ARG B 70 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 66 time to evaluate : 0.546 Fit side-chains revert: symmetry clash REVERT: A 157 TYR cc_start: 0.8566 (t80) cc_final: 0.8305 (t80) REVERT: A 253 PHE cc_start: 0.9094 (OUTLIER) cc_final: 0.8695 (m-80) REVERT: A 381 MET cc_start: 0.8151 (mtm) cc_final: 0.7946 (mtp) REVERT: A 511 LYS cc_start: 0.8095 (tttt) cc_final: 0.7473 (mttp) outliers start: 9 outliers final: 4 residues processed: 71 average time/residue: 1.2592 time to fit residues: 92.9819 Evaluate side-chains 65 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 60 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 PHE Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 40 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 29 optimal weight: 3.9990 chunk 16 optimal weight: 0.4980 chunk 43 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 52 optimal weight: 0.0000 chunk 57 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN A 246 GLN A 330 ASN A 355 ASN A 422 ASN C 28 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4782 Z= 0.171 Angle : 0.497 6.651 6506 Z= 0.264 Chirality : 0.039 0.148 736 Planarity : 0.004 0.042 795 Dihedral : 4.790 47.274 647 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.60 % Allowed : 15.03 % Favored : 83.37 % 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: 0.71 (0.35), residues: 586 helix: 1.53 (0.28), residues: 347 sheet: -0.87 (0.59), residues: 65 loop : -1.11 (0.47), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 108 HIS 0.002 0.001 HIS B 38 PHE 0.016 0.001 PHE A 144 TYR 0.024 0.001 TYR A 117 ARG 0.002 0.000 ARG A 106 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 63 time to evaluate : 0.530 Fit side-chains REVERT: A 157 TYR cc_start: 0.8520 (t80) cc_final: 0.8259 (t80) REVERT: A 223 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.7369 (ttt90) REVERT: A 253 PHE cc_start: 0.9066 (OUTLIER) cc_final: 0.8695 (m-80) REVERT: A 381 MET cc_start: 0.8096 (mtm) cc_final: 0.7871 (mtp) REVERT: A 511 LYS cc_start: 0.8106 (tttt) cc_final: 0.7509 (mttp) outliers start: 8 outliers final: 5 residues processed: 67 average time/residue: 1.2296 time to fit residues: 85.7733 Evaluate side-chains 69 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 62 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 253 PHE Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain C residue 92 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 25 optimal weight: 0.1980 chunk 35 optimal weight: 1.9990 chunk 52 optimal weight: 0.0470 chunk 56 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN A 330 ASN A 422 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4782 Z= 0.186 Angle : 0.490 6.576 6506 Z= 0.259 Chirality : 0.039 0.150 736 Planarity : 0.004 0.046 795 Dihedral : 4.718 45.020 647 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.20 % Allowed : 15.43 % Favored : 82.36 % 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: 1.26 (0.35), residues: 586 helix: 1.89 (0.28), residues: 347 sheet: -0.72 (0.59), residues: 66 loop : -0.65 (0.48), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 148 HIS 0.003 0.001 HIS B 38 PHE 0.016 0.001 PHE A 144 TYR 0.024 0.001 TYR A 117 ARG 0.002 0.000 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 66 time to evaluate : 0.531 Fit side-chains revert: symmetry clash REVERT: A 223 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.7376 (ttt90) REVERT: A 447 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7467 (mm-30) REVERT: A 511 LYS cc_start: 0.8051 (tttt) cc_final: 0.7467 (mttp) outliers start: 11 outliers final: 6 residues processed: 72 average time/residue: 1.2216 time to fit residues: 91.5704 Evaluate side-chains 72 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 65 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 92 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 41 optimal weight: 0.3980 chunk 23 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 50 optimal weight: 0.4980 chunk 14 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4782 Z= 0.183 Angle : 0.491 6.599 6506 Z= 0.257 Chirality : 0.039 0.151 736 Planarity : 0.004 0.050 795 Dihedral : 4.174 16.016 645 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.80 % Allowed : 16.63 % Favored : 81.56 % 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: 1.54 (0.35), residues: 586 helix: 2.05 (0.27), residues: 347 sheet: -0.42 (0.60), residues: 66 loop : -0.48 (0.49), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 148 HIS 0.003 0.001 HIS B 38 PHE 0.015 0.001 PHE A 144 TYR 0.024 0.001 TYR A 117 ARG 0.001 0.000 ARG A 518 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 64 time to evaluate : 0.527 Fit side-chains revert: symmetry clash REVERT: A 106 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7935 (mtt90) REVERT: A 223 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.7405 (ttt90) REVERT: A 420 ASN cc_start: 0.7570 (p0) cc_final: 0.7366 (p0) REVERT: A 511 LYS cc_start: 0.8070 (tttt) cc_final: 0.7483 (mttp) outliers start: 9 outliers final: 7 residues processed: 69 average time/residue: 1.2410 time to fit residues: 89.0626 Evaluate side-chains 72 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 63 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ARG Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 92 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 13 optimal weight: 0.5980 chunk 56 optimal weight: 0.1980 chunk 46 optimal weight: 2.9990 chunk 25 optimal weight: 0.4980 chunk 4 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 54 optimal weight: 0.0570 chunk 6 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 overall best weight: 0.3898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4782 Z= 0.148 Angle : 0.466 6.422 6506 Z= 0.244 Chirality : 0.039 0.149 736 Planarity : 0.004 0.051 795 Dihedral : 3.987 15.781 645 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.00 % Allowed : 16.03 % Favored : 81.96 % 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: 1.85 (0.36), residues: 586 helix: 2.25 (0.28), residues: 347 sheet: 0.03 (0.62), residues: 66 loop : -0.39 (0.50), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 148 HIS 0.003 0.001 HIS B 38 PHE 0.013 0.001 PHE A 144 TYR 0.025 0.001 TYR A 117 ARG 0.002 0.000 ARG A 518 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 68 time to evaluate : 0.490 Fit side-chains revert: symmetry clash REVERT: A 106 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7931 (mtt90) REVERT: A 223 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.7431 (ttt90) REVERT: A 253 PHE cc_start: 0.9067 (OUTLIER) cc_final: 0.8679 (m-80) REVERT: A 447 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7485 (mm-30) REVERT: A 511 LYS cc_start: 0.8067 (tttt) cc_final: 0.7476 (mttp) outliers start: 10 outliers final: 6 residues processed: 74 average time/residue: 1.2560 time to fit residues: 96.8775 Evaluate side-chains 74 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 65 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ARG Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 253 PHE Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 92 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 31 optimal weight: 1.9990 chunk 47 optimal weight: 0.0870 chunk 55 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 16 optimal weight: 0.0870 chunk 10 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 overall best weight: 0.5336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN A 422 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4782 Z= 0.181 Angle : 0.485 6.556 6506 Z= 0.253 Chirality : 0.039 0.151 736 Planarity : 0.004 0.051 795 Dihedral : 4.035 16.136 645 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.20 % Allowed : 16.83 % Favored : 80.96 % 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: 1.88 (0.35), residues: 586 helix: 2.24 (0.27), residues: 347 sheet: 0.11 (0.63), residues: 66 loop : -0.29 (0.50), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 39 HIS 0.003 0.001 HIS B 38 PHE 0.014 0.001 PHE A 144 TYR 0.024 0.001 TYR A 117 ARG 0.002 0.000 ARG A 518 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 63 time to evaluate : 0.485 Fit side-chains revert: symmetry clash REVERT: A 106 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7947 (mtt90) REVERT: A 223 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7435 (ttt90) REVERT: A 447 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7485 (mm-30) REVERT: A 511 LYS cc_start: 0.8068 (tttt) cc_final: 0.7446 (mttp) outliers start: 11 outliers final: 8 residues processed: 70 average time/residue: 1.2086 time to fit residues: 88.0817 Evaluate side-chains 73 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 63 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ARG Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 92 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 50 optimal weight: 0.4980 chunk 53 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 52 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 40 optimal weight: 0.4980 chunk 15 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN C 28 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4782 Z= 0.237 Angle : 0.515 6.672 6506 Z= 0.269 Chirality : 0.041 0.154 736 Planarity : 0.004 0.050 795 Dihedral : 4.214 17.749 645 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.00 % Allowed : 17.03 % Favored : 80.96 % 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: 1.74 (0.36), residues: 586 helix: 2.07 (0.28), residues: 348 sheet: 0.10 (0.64), residues: 66 loop : -0.27 (0.51), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 39 HIS 0.003 0.001 HIS B 38 PHE 0.016 0.002 PHE A 144 TYR 0.024 0.001 TYR A 117 ARG 0.003 0.000 ARG A 518 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 63 time to evaluate : 0.527 Fit side-chains revert: symmetry clash REVERT: A 106 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.8055 (mtt90) REVERT: A 223 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7412 (ttt90) REVERT: A 447 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7529 (mm-30) REVERT: A 511 LYS cc_start: 0.8071 (tttt) cc_final: 0.7461 (mttp) outliers start: 10 outliers final: 8 residues processed: 69 average time/residue: 1.2758 time to fit residues: 91.6383 Evaluate side-chains 73 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 63 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ARG Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 92 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 3.9990 chunk 49 optimal weight: 8.9990 chunk 51 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 55 optimal weight: 0.4980 chunk 33 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 ASN A 422 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4782 Z= 0.209 Angle : 0.499 6.634 6506 Z= 0.261 Chirality : 0.040 0.152 736 Planarity : 0.004 0.051 795 Dihedral : 4.127 16.328 645 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.00 % Allowed : 17.03 % Favored : 80.96 % 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: 1.79 (0.36), residues: 586 helix: 2.13 (0.28), residues: 347 sheet: 0.07 (0.64), residues: 66 loop : -0.26 (0.50), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 39 HIS 0.003 0.001 HIS B 38 PHE 0.015 0.002 PHE A 144 TYR 0.024 0.001 TYR A 117 ARG 0.002 0.000 ARG A 518 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 64 time to evaluate : 0.497 Fit side-chains revert: symmetry clash REVERT: A 106 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.8057 (mtt90) REVERT: A 223 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.7409 (ttt90) REVERT: A 444 LEU cc_start: 0.8615 (mm) cc_final: 0.8077 (mt) REVERT: A 511 LYS cc_start: 0.8069 (tttt) cc_final: 0.7456 (mttp) outliers start: 10 outliers final: 8 residues processed: 70 average time/residue: 1.2189 time to fit residues: 88.8582 Evaluate side-chains 74 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 64 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ARG Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 92 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 4 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 49 optimal weight: 9.9990 chunk 14 optimal weight: 0.5980 chunk 42 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 46 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4782 Z= 0.206 Angle : 0.500 6.624 6506 Z= 0.261 Chirality : 0.040 0.152 736 Planarity : 0.004 0.051 795 Dihedral : 4.125 16.686 645 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.00 % Allowed : 17.43 % Favored : 80.56 % 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: 1.78 (0.36), residues: 586 helix: 2.12 (0.28), residues: 347 sheet: 0.10 (0.64), residues: 66 loop : -0.26 (0.50), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 39 HIS 0.003 0.001 HIS B 38 PHE 0.015 0.002 PHE A 144 TYR 0.024 0.001 TYR A 117 ARG 0.002 0.000 ARG A 518 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 63 time to evaluate : 0.556 Fit side-chains revert: symmetry clash REVERT: A 106 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.8059 (mtt90) REVERT: A 223 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.7409 (ttt90) REVERT: A 444 LEU cc_start: 0.8595 (mm) cc_final: 0.8050 (mt) REVERT: A 447 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7508 (mm-30) REVERT: A 511 LYS cc_start: 0.8062 (tttt) cc_final: 0.7446 (mttp) outliers start: 10 outliers final: 8 residues processed: 69 average time/residue: 1.1922 time to fit residues: 85.8059 Evaluate side-chains 73 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 63 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ARG Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 92 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 52 optimal weight: 0.0370 chunk 30 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.165866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.115455 restraints weight = 4811.649| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.93 r_work: 0.3105 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4782 Z= 0.173 Angle : 0.486 7.233 6506 Z= 0.253 Chirality : 0.039 0.150 736 Planarity : 0.004 0.051 795 Dihedral : 4.024 16.757 645 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.80 % Allowed : 17.43 % Favored : 80.76 % 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: 1.88 (0.36), residues: 586 helix: 2.23 (0.28), residues: 347 sheet: 0.15 (0.63), residues: 66 loop : -0.31 (0.50), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 39 HIS 0.003 0.001 HIS B 38 PHE 0.014 0.001 PHE A 144 TYR 0.024 0.001 TYR A 117 ARG 0.002 0.000 ARG A 518 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2280.68 seconds wall clock time: 40 minutes 43.23 seconds (2443.23 seconds total)