Starting phenix.real_space_refine on Tue Mar 11 19:19:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pdf_13336/03_2025/7pdf_13336.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pdf_13336/03_2025/7pdf_13336.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pdf_13336/03_2025/7pdf_13336.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pdf_13336/03_2025/7pdf_13336.map" model { file = "/net/cci-nas-00/data/ceres_data/7pdf_13336/03_2025/7pdf_13336.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pdf_13336/03_2025/7pdf_13336.cif" } resolution = 3.8 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 81 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 46 5.16 5 C 4055 2.51 5 N 1107 2.21 5 O 1215 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6427 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3585 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 443} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2809 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 13, 'TRANS': 327} Chain breaks: 1 Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GSP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.83, per 1000 atoms: 0.75 Number of scatterers: 6427 At special positions: 0 Unit cell: (109.35, 105.3, 102.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 46 16.00 P 3 15.00 Mg 1 11.99 O 1215 8.00 N 1107 7.00 C 4055 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.73 Conformation dependent library (CDL) restraints added in 985.5 milliseconds 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1494 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 5 sheets defined 47.6% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 321 through 336 removed outlier: 4.198A pdb=" N VAL A 325 " --> pdb=" O LYS A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 346 Processing helix chain 'A' and resid 354 through 359 Processing helix chain 'A' and resid 402 through 407 Processing helix chain 'A' and resid 413 through 434 Processing helix chain 'A' and resid 457 through 478 Processing helix chain 'A' and resid 511 through 523 removed outlier: 4.120A pdb=" N ASN A 515 " --> pdb=" O SER A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 537 Processing helix chain 'A' and resid 1021 through 1037 removed outlier: 4.073A pdb=" N MET A1025 " --> pdb=" O LYS A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1048 removed outlier: 3.758A pdb=" N LYS A1046 " --> pdb=" O ALA A1042 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N VAL A1047 " --> pdb=" O GLU A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1098 removed outlier: 3.681A pdb=" N TYR A1083 " --> pdb=" O GLY A1079 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASP A1092 " --> pdb=" O GLU A1088 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE A1093 " --> pdb=" O LEU A1089 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER A1098 " --> pdb=" O ASP A1094 " (cutoff:3.500A) Processing helix chain 'A' and resid 1131 through 1133 No H-bonds generated for 'chain 'A' and resid 1131 through 1133' Processing helix chain 'A' and resid 1134 through 1156 Processing helix chain 'A' and resid 1190 through 1201 Processing helix chain 'A' and resid 1211 through 1219 removed outlier: 4.089A pdb=" N LYS A1219 " --> pdb=" O ARG A1215 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 38 Processing helix chain 'B' and resid 52 through 65 Processing helix chain 'B' and resid 89 through 110 removed outlier: 4.031A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 123 No H-bonds generated for 'chain 'B' and resid 121 through 123' Processing helix chain 'B' and resid 124 through 134 Processing helix chain 'B' and resid 143 through 156 removed outlier: 3.677A pdb=" N ASP B 156 " --> pdb=" O ALA B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 165 removed outlier: 3.623A pdb=" N ARG B 165 " --> pdb=" O ALA B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 184 removed outlier: 3.650A pdb=" N ASP B 180 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL B 184 " --> pdb=" O ASP B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 187 No H-bonds generated for 'chain 'B' and resid 185 through 187' Processing helix chain 'B' and resid 193 through 199 Processing helix chain 'B' and resid 233 through 237 Processing helix chain 'B' and resid 264 through 278 removed outlier: 3.534A pdb=" N ASN B 278 " --> pdb=" O LYS B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 304 removed outlier: 3.563A pdb=" N LEU B 297 " --> pdb=" O LYS B 293 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY B 304 " --> pdb=" O LYS B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 312 Processing helix chain 'B' and resid 313 through 316 removed outlier: 3.549A pdb=" N ALA B 316 " --> pdb=" O PRO B 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 313 through 316' Processing helix chain 'B' and resid 331 through 347 Processing helix chain 'B' and resid 368 through 388 removed outlier: 3.854A pdb=" N LEU B 388 " --> pdb=" O GLN B 384 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 436 through 439 removed outlier: 7.265A pdb=" N TYR A 446 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N GLN A 389 " --> pdb=" O CYS A 497 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N CYS A 497 " --> pdb=" O GLN A 389 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N GLU A 391 " --> pdb=" O VAL A 495 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N VAL A 495 " --> pdb=" O GLU A 391 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 436 through 439 removed outlier: 7.265A pdb=" N TYR A 446 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N GLN A 389 " --> pdb=" O CYS A 497 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N CYS A 497 " --> pdb=" O GLN A 389 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N GLU A 391 " --> pdb=" O VAL A 495 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N VAL A 495 " --> pdb=" O GLU A 391 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N HIS A 530 " --> pdb=" O MET A 486 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL A 488 " --> pdb=" O HIS A 530 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1052 through 1055 Processing sheet with id=AA4, first strand: chain 'A' and resid 1106 through 1109 removed outlier: 7.214A pdb=" N MET A1116 " --> pdb=" O ILE A1108 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N HIS A1170 " --> pdb=" O SER A1210 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR A1240 " --> pdb=" O GLY A1228 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLY A1228 " --> pdb=" O THR A1240 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LEU A1242 " --> pdb=" O TYR A1226 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N TYR A1226 " --> pdb=" O LEU A1242 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 208 through 213 removed outlier: 5.891A pdb=" N HIS B 41 " --> pdb=" O HIS B 220 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N PHE B 222 " --> pdb=" O HIS B 41 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N LEU B 43 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N ALA B 243 " --> pdb=" O THR B 40 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ARG B 42 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE B 245 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LEU B 44 " --> pdb=" O ILE B 245 " (cutoff:3.500A) 309 hydrogen bonds defined for protein. 891 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: 2.12 Time building geometry restraints manager: 2.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1988 1.33 - 1.45: 969 1.45 - 1.57: 3514 1.57 - 1.69: 5 1.69 - 1.81: 72 Bond restraints: 6548 Sorted by residual: bond pdb=" CB GLU A1088 " pdb=" CG GLU A1088 " ideal model delta sigma weight residual 1.520 1.472 0.048 3.00e-02 1.11e+03 2.53e+00 bond pdb=" CB GLN B 59 " pdb=" CG GLN B 59 " ideal model delta sigma weight residual 1.520 1.473 0.047 3.00e-02 1.11e+03 2.41e+00 bond pdb=" CB TRP A 510 " pdb=" CG TRP A 510 " ideal model delta sigma weight residual 1.498 1.454 0.044 3.10e-02 1.04e+03 2.05e+00 bond pdb=" CG1 ILE B 288 " pdb=" CD1 ILE B 288 " ideal model delta sigma weight residual 1.513 1.458 0.055 3.90e-02 6.57e+02 2.02e+00 bond pdb=" CB TRP A1188 " pdb=" CG TRP A1188 " ideal model delta sigma weight residual 1.498 1.457 0.041 3.10e-02 1.04e+03 1.77e+00 ... (remaining 6543 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 8631 2.38 - 4.77: 180 4.77 - 7.15: 16 7.15 - 9.53: 2 9.53 - 11.91: 1 Bond angle restraints: 8830 Sorted by residual: angle pdb=" C LYS A 437 " pdb=" N ILE A 438 " pdb=" CA ILE A 438 " ideal model delta sigma weight residual 123.16 118.62 4.54 1.06e+00 8.90e-01 1.83e+01 angle pdb=" C TYR A 445 " pdb=" N TYR A 446 " pdb=" CA TYR A 446 " ideal model delta sigma weight residual 121.75 115.52 6.23 1.73e+00 3.34e-01 1.30e+01 angle pdb=" N ILE A1178 " pdb=" CA ILE A1178 " pdb=" C ILE A1178 " ideal model delta sigma weight residual 110.74 113.98 -3.24 9.10e-01 1.21e+00 1.27e+01 angle pdb=" CA LEU A 496 " pdb=" CB LEU A 496 " pdb=" CG LEU A 496 " ideal model delta sigma weight residual 116.30 128.21 -11.91 3.50e+00 8.16e-02 1.16e+01 angle pdb=" C1' GSP B 501 " pdb=" C2' GSP B 501 " pdb=" C3' GSP B 501 " ideal model delta sigma weight residual 111.00 102.48 8.52 3.00e+00 1.11e-01 8.07e+00 ... (remaining 8825 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.01: 3469 17.01 - 34.02: 398 34.02 - 51.03: 75 51.03 - 68.05: 10 68.05 - 85.06: 5 Dihedral angle restraints: 3957 sinusoidal: 1643 harmonic: 2314 Sorted by residual: dihedral pdb=" CA VAL B 114 " pdb=" C VAL B 114 " pdb=" N PRO B 115 " pdb=" CA PRO B 115 " ideal model delta harmonic sigma weight residual 180.00 150.19 29.81 0 5.00e+00 4.00e-02 3.56e+01 dihedral pdb=" CA SER A 511 " pdb=" C SER A 511 " pdb=" N ASN A 512 " pdb=" CA ASN A 512 " ideal model delta harmonic sigma weight residual 180.00 154.98 25.02 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA VAL A1177 " pdb=" C VAL A1177 " pdb=" N ILE A1178 " pdb=" CA ILE A1178 " ideal model delta harmonic sigma weight residual -180.00 -156.22 -23.78 0 5.00e+00 4.00e-02 2.26e+01 ... (remaining 3954 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 540 0.037 - 0.073: 293 0.073 - 0.110: 102 0.110 - 0.146: 21 0.146 - 0.183: 3 Chirality restraints: 959 Sorted by residual: chirality pdb=" C2' GSP B 501 " pdb=" C1' GSP B 501 " pdb=" C3' GSP B 501 " pdb=" O2' GSP B 501 " both_signs ideal model delta sigma weight residual False -2.47 -2.65 0.18 2.00e-01 2.50e+01 8.37e-01 chirality pdb=" C3' GSP B 501 " pdb=" C2' GSP B 501 " pdb=" C4' GSP B 501 " pdb=" O3' GSP B 501 " both_signs ideal model delta sigma weight residual False -2.47 -2.65 0.18 2.00e-01 2.50e+01 8.28e-01 chirality pdb=" CB ILE B 235 " pdb=" CA ILE B 235 " pdb=" CG1 ILE B 235 " pdb=" CG2 ILE B 235 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.39e-01 ... (remaining 956 not shown) Planarity restraints: 1140 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A1037 " -0.031 5.00e-02 4.00e+02 4.68e-02 3.51e+00 pdb=" N PRO A1038 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A1038 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A1038 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 385 " -0.006 2.00e-02 2.50e+03 1.19e-02 2.48e+00 pdb=" CG PHE A 385 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE A 385 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE A 385 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE A 385 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 385 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE A 385 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 114 " -0.024 5.00e-02 4.00e+02 3.63e-02 2.11e+00 pdb=" N PRO B 115 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO B 115 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 115 " -0.020 5.00e-02 4.00e+02 ... (remaining 1137 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 71 2.49 - 3.09: 5038 3.09 - 3.69: 10076 3.69 - 4.30: 14353 4.30 - 4.90: 23454 Nonbonded interactions: 52992 Sorted by model distance: nonbonded pdb=" O2G GSP B 501 " pdb="MG MG B 502 " model vdw 1.885 2.170 nonbonded pdb=" O2B GSP B 501 " pdb="MG MG B 502 " model vdw 1.916 2.170 nonbonded pdb=" O ALA A 412 " pdb=" OG SER A1052 " model vdw 2.074 3.040 nonbonded pdb=" OE2 GLU A1211 " pdb=" NH2 ARG A1215 " model vdw 2.142 3.120 nonbonded pdb=" O1B GSP B 501 " pdb="MG MG B 502 " model vdw 2.151 2.170 ... (remaining 52987 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.160 Find NCS groups from input model: 0.070 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: 0.000 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 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 : 0.008 0.055 6548 Z= 0.529 Angle : 0.829 11.913 8830 Z= 0.465 Chirality : 0.048 0.183 959 Planarity : 0.004 0.047 1140 Dihedral : 14.632 85.056 2463 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.10 % Favored : 89.90 % Rotamer: Outliers : 0.29 % Allowed : 12.36 % Favored : 87.36 % 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: -4.24 (0.24), residues: 782 helix: -2.27 (0.21), residues: 368 sheet: -2.71 (0.40), residues: 121 loop : -3.38 (0.29), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 277 HIS 0.010 0.002 HIS B 220 PHE 0.025 0.002 PHE A 385 TYR 0.020 0.002 TYR A1083 ARG 0.006 0.001 ARG A1026 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 124 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 MET cc_start: 0.8712 (tpp) cc_final: 0.8231 (mmt) REVERT: A 413 HIS cc_start: 0.8168 (t70) cc_final: 0.7753 (t-90) REVERT: A 1094 ASP cc_start: 0.8101 (m-30) cc_final: 0.7700 (m-30) REVERT: A 1106 GLU cc_start: 0.8256 (mp0) cc_final: 0.7773 (mp0) REVERT: A 1136 LEU cc_start: 0.9520 (mt) cc_final: 0.9212 (mt) REVERT: A 1157 MET cc_start: 0.8314 (tpp) cc_final: 0.7724 (tpp) REVERT: B 151 LYS cc_start: 0.7686 (mmpt) cc_final: 0.7471 (mmtt) outliers start: 2 outliers final: 2 residues processed: 125 average time/residue: 0.2214 time to fit residues: 35.1938 Evaluate side-chains 90 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 88 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain B residue 114 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 33 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 40 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 61 optimal weight: 0.0370 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 420 ASN A 458 HIS A1040 HIS A1044 GLN B 41 HIS B 64 HIS B 98 ASN B 124 ASN B 136 ASN B 267 GLN B 271 ASN B 294 GLN B 362 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.117856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.093027 restraints weight = 14028.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.095807 restraints weight = 7699.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.097741 restraints weight = 5322.005| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6548 Z= 0.203 Angle : 0.616 8.195 8830 Z= 0.320 Chirality : 0.043 0.158 959 Planarity : 0.004 0.055 1140 Dihedral : 5.397 48.283 884 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.87 % Allowed : 14.80 % Favored : 83.33 % 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: -2.39 (0.28), residues: 782 helix: -0.43 (0.26), residues: 377 sheet: -2.38 (0.41), residues: 123 loop : -2.70 (0.32), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1159 HIS 0.003 0.001 HIS A 530 PHE 0.013 0.001 PHE A1142 TYR 0.014 0.002 TYR B 163 ARG 0.004 0.000 ARG B 389 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 129 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7233 (tp30) REVERT: A 333 MET cc_start: 0.8734 (tpp) cc_final: 0.8250 (mmt) REVERT: A 413 HIS cc_start: 0.8119 (t70) cc_final: 0.7690 (t-90) REVERT: A 464 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7748 (mt-10) REVERT: A 1094 ASP cc_start: 0.8163 (m-30) cc_final: 0.7791 (m-30) REVERT: A 1136 LEU cc_start: 0.9231 (mt) cc_final: 0.8990 (mt) REVERT: A 1157 MET cc_start: 0.8005 (tpp) cc_final: 0.7227 (tpp) REVERT: B 59 GLN cc_start: 0.8359 (tp-100) cc_final: 0.7957 (tp40) REVERT: B 125 GLN cc_start: 0.8152 (tp40) cc_final: 0.7727 (tp-100) REVERT: B 198 LEU cc_start: 0.9198 (mt) cc_final: 0.8629 (mt) outliers start: 13 outliers final: 4 residues processed: 137 average time/residue: 0.1731 time to fit residues: 32.2384 Evaluate side-chains 106 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 102 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1110 THR Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 379 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 29 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 52 optimal weight: 7.9990 chunk 31 optimal weight: 0.1980 chunk 64 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 55 optimal weight: 0.9990 chunk 76 optimal weight: 0.0970 chunk 66 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.119143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.094395 restraints weight = 14337.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.097302 restraints weight = 7773.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.099209 restraints weight = 5327.816| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6548 Z= 0.181 Angle : 0.592 9.217 8830 Z= 0.305 Chirality : 0.043 0.147 959 Planarity : 0.003 0.052 1140 Dihedral : 5.019 46.614 882 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.16 % Allowed : 19.83 % Favored : 78.02 % 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: -1.65 (0.29), residues: 782 helix: 0.21 (0.27), residues: 378 sheet: -2.12 (0.39), residues: 137 loop : -2.32 (0.34), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1159 HIS 0.003 0.001 HIS B 220 PHE 0.015 0.001 PHE B 140 TYR 0.016 0.001 TYR B 130 ARG 0.003 0.000 ARG B 389 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 2.614 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 324 GLU cc_start: 0.8070 (pp20) cc_final: 0.7300 (tm-30) REVERT: A 326 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7355 (tp30) REVERT: A 333 MET cc_start: 0.8703 (tpp) cc_final: 0.8304 (mmt) REVERT: A 413 HIS cc_start: 0.8107 (t70) cc_final: 0.7701 (t-90) REVERT: A 464 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7800 (mt-10) REVERT: A 1094 ASP cc_start: 0.8161 (m-30) cc_final: 0.7869 (m-30) REVERT: A 1136 LEU cc_start: 0.9173 (mt) cc_final: 0.8941 (mt) REVERT: A 1157 MET cc_start: 0.7852 (tpp) cc_final: 0.7368 (tpp) REVERT: B 110 MET cc_start: 0.8583 (mtp) cc_final: 0.8259 (mtt) REVERT: B 125 GLN cc_start: 0.7989 (tp40) cc_final: 0.7513 (tp-100) outliers start: 15 outliers final: 8 residues processed: 134 average time/residue: 0.1869 time to fit residues: 34.7235 Evaluate side-chains 106 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1110 THR Chi-restraints excluded: chain A residue 1138 ILE Chi-restraints excluded: chain A residue 1151 ASP Chi-restraints excluded: chain A residue 1183 LEU Chi-restraints excluded: chain B residue 114 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 60 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 491 HIS ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.118662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.093953 restraints weight = 14289.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.096703 restraints weight = 7821.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.098585 restraints weight = 5426.720| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6548 Z= 0.214 Angle : 0.607 9.982 8830 Z= 0.309 Chirality : 0.043 0.156 959 Planarity : 0.003 0.054 1140 Dihedral : 4.933 46.873 882 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.73 % Allowed : 21.55 % Favored : 75.72 % 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: -1.42 (0.29), residues: 782 helix: 0.38 (0.27), residues: 380 sheet: -2.06 (0.39), residues: 139 loop : -2.17 (0.35), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1159 HIS 0.011 0.001 HIS B 387 PHE 0.011 0.001 PHE B 140 TYR 0.011 0.001 TYR A1214 ARG 0.003 0.000 ARG B 389 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 GLU cc_start: 0.8045 (pp20) cc_final: 0.7328 (tm-30) REVERT: A 413 HIS cc_start: 0.8126 (t70) cc_final: 0.7697 (t-90) REVERT: A 464 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7767 (mt-10) REVERT: A 1094 ASP cc_start: 0.8169 (m-30) cc_final: 0.7896 (m-30) REVERT: A 1136 LEU cc_start: 0.9203 (mt) cc_final: 0.8962 (mt) REVERT: A 1157 MET cc_start: 0.7783 (tpp) cc_final: 0.6997 (tpp) REVERT: B 110 MET cc_start: 0.8616 (mtp) cc_final: 0.8321 (mtt) REVERT: B 125 GLN cc_start: 0.7904 (tp40) cc_final: 0.7434 (pt0) outliers start: 19 outliers final: 10 residues processed: 119 average time/residue: 0.1646 time to fit residues: 26.9491 Evaluate side-chains 110 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 1110 THR Chi-restraints excluded: chain A residue 1138 ILE Chi-restraints excluded: chain A residue 1151 ASP Chi-restraints excluded: chain A residue 1183 LEU Chi-restraints excluded: chain A residue 1232 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 379 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 0 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 27 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.112463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.089187 restraints weight = 14315.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.091528 restraints weight = 8119.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.093075 restraints weight = 5706.243| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 6548 Z= 0.352 Angle : 0.657 10.101 8830 Z= 0.339 Chirality : 0.045 0.168 959 Planarity : 0.004 0.053 1140 Dihedral : 5.167 47.014 882 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 3.30 % Allowed : 22.13 % Favored : 74.57 % 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: -1.36 (0.29), residues: 782 helix: 0.38 (0.27), residues: 377 sheet: -1.99 (0.40), residues: 131 loop : -2.07 (0.34), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 281 HIS 0.010 0.001 HIS B 387 PHE 0.011 0.002 PHE A1168 TYR 0.016 0.002 TYR A1083 ARG 0.004 0.001 ARG A1026 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 104 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 GLU cc_start: 0.8104 (pp20) cc_final: 0.7405 (tm-30) REVERT: A 570 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8564 (mp) REVERT: A 1094 ASP cc_start: 0.8206 (m-30) cc_final: 0.7904 (m-30) REVERT: A 1136 LEU cc_start: 0.9353 (mt) cc_final: 0.9096 (mt) REVERT: A 1157 MET cc_start: 0.7903 (tpp) cc_final: 0.7329 (tpp) REVERT: B 110 MET cc_start: 0.8664 (mtp) cc_final: 0.8345 (mtt) REVERT: B 125 GLN cc_start: 0.7853 (tp40) cc_final: 0.7413 (pt0) outliers start: 23 outliers final: 13 residues processed: 118 average time/residue: 0.1698 time to fit residues: 27.6457 Evaluate side-chains 108 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 1050 THR Chi-restraints excluded: chain A residue 1110 THR Chi-restraints excluded: chain A residue 1138 ILE Chi-restraints excluded: chain A residue 1151 ASP Chi-restraints excluded: chain A residue 1183 LEU Chi-restraints excluded: chain A residue 1232 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 379 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 18 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 77 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.118478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.093894 restraints weight = 14189.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.096701 restraints weight = 7692.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.098543 restraints weight = 5317.712| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6548 Z= 0.206 Angle : 0.613 11.054 8830 Z= 0.311 Chirality : 0.043 0.233 959 Planarity : 0.003 0.050 1140 Dihedral : 4.960 46.902 882 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.87 % Allowed : 23.42 % Favored : 73.71 % 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: -1.14 (0.29), residues: 782 helix: 0.50 (0.27), residues: 378 sheet: -1.89 (0.40), residues: 131 loop : -1.85 (0.35), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1159 HIS 0.012 0.001 HIS B 387 PHE 0.010 0.001 PHE B 376 TYR 0.019 0.001 TYR A1214 ARG 0.002 0.000 ARG A1215 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 322 ASP cc_start: 0.7448 (p0) cc_final: 0.6134 (p0) REVERT: A 324 GLU cc_start: 0.8011 (pp20) cc_final: 0.7396 (pp20) REVERT: A 413 HIS cc_start: 0.8205 (t-90) cc_final: 0.7805 (t-90) REVERT: A 464 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7755 (mt-10) REVERT: A 1094 ASP cc_start: 0.8179 (m-30) cc_final: 0.7889 (m-30) REVERT: A 1157 MET cc_start: 0.7799 (tpp) cc_final: 0.6958 (tpp) REVERT: B 110 MET cc_start: 0.8546 (mtp) cc_final: 0.8273 (mtt) REVERT: B 125 GLN cc_start: 0.7852 (tp40) cc_final: 0.7440 (pt0) outliers start: 20 outliers final: 14 residues processed: 120 average time/residue: 0.1631 time to fit residues: 27.1823 Evaluate side-chains 114 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 1095 GLU Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1110 THR Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1151 ASP Chi-restraints excluded: chain A residue 1232 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 379 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 15 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 60 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 65 optimal weight: 0.4980 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.118374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.093879 restraints weight = 14143.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.096660 restraints weight = 7842.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.098460 restraints weight = 5442.569| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6548 Z= 0.218 Angle : 0.613 11.651 8830 Z= 0.311 Chirality : 0.043 0.146 959 Planarity : 0.003 0.047 1140 Dihedral : 4.897 47.151 882 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.30 % Allowed : 23.42 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.30), residues: 782 helix: 0.60 (0.27), residues: 379 sheet: -1.84 (0.40), residues: 130 loop : -1.69 (0.36), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1159 HIS 0.011 0.001 HIS B 387 PHE 0.010 0.001 PHE A1168 TYR 0.018 0.001 TYR A1214 ARG 0.002 0.000 ARG A1084 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.808 Fit side-chains revert: symmetry clash REVERT: A 322 ASP cc_start: 0.7530 (p0) cc_final: 0.6285 (p0) REVERT: A 324 GLU cc_start: 0.8080 (pp20) cc_final: 0.7491 (pp20) REVERT: A 413 HIS cc_start: 0.8285 (t-90) cc_final: 0.7868 (t-90) REVERT: A 1094 ASP cc_start: 0.8179 (m-30) cc_final: 0.7923 (m-30) REVERT: A 1147 MET cc_start: 0.8125 (mmm) cc_final: 0.7919 (tpp) REVERT: B 110 MET cc_start: 0.8626 (mtp) cc_final: 0.8352 (mtt) REVERT: B 125 GLN cc_start: 0.7814 (tp40) cc_final: 0.7415 (pt0) outliers start: 23 outliers final: 18 residues processed: 125 average time/residue: 0.1613 time to fit residues: 27.9443 Evaluate side-chains 119 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 1036 ILE Chi-restraints excluded: chain A residue 1095 GLU Chi-restraints excluded: chain A residue 1110 THR Chi-restraints excluded: chain A residue 1138 ILE Chi-restraints excluded: chain A residue 1151 ASP Chi-restraints excluded: chain A residue 1183 LEU Chi-restraints excluded: chain A residue 1232 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 379 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 48 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.118038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.093448 restraints weight = 14181.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.096197 restraints weight = 7882.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.097997 restraints weight = 5490.020| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 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 : 0.004 0.036 6548 Z= 0.242 Angle : 0.642 12.407 8830 Z= 0.326 Chirality : 0.044 0.146 959 Planarity : 0.003 0.049 1140 Dihedral : 4.934 45.361 882 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.30 % Allowed : 23.85 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.29), residues: 782 helix: 0.58 (0.27), residues: 376 sheet: -1.58 (0.41), residues: 136 loop : -1.81 (0.35), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1159 HIS 0.011 0.001 HIS B 387 PHE 0.010 0.001 PHE A1168 TYR 0.018 0.001 TYR A1214 ARG 0.003 0.000 ARG A1084 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.721 Fit side-chains revert: symmetry clash REVERT: A 322 ASP cc_start: 0.7246 (p0) cc_final: 0.5966 (p0) REVERT: A 324 GLU cc_start: 0.7948 (pp20) cc_final: 0.7304 (pp20) REVERT: A 413 HIS cc_start: 0.8159 (t-90) cc_final: 0.7741 (t-90) REVERT: A 570 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8545 (mp) REVERT: A 1094 ASP cc_start: 0.8118 (m-30) cc_final: 0.7833 (m-30) REVERT: A 1157 MET cc_start: 0.7334 (tpp) cc_final: 0.6812 (ttm) REVERT: B 110 MET cc_start: 0.8507 (mtp) cc_final: 0.8246 (mtt) REVERT: B 125 GLN cc_start: 0.7755 (tp40) cc_final: 0.7466 (pt0) REVERT: B 135 MET cc_start: 0.8284 (ppp) cc_final: 0.8036 (ppp) outliers start: 23 outliers final: 18 residues processed: 117 average time/residue: 0.1442 time to fit residues: 24.3308 Evaluate side-chains 116 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 1036 ILE Chi-restraints excluded: chain A residue 1095 GLU Chi-restraints excluded: chain A residue 1110 THR Chi-restraints excluded: chain A residue 1138 ILE Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1151 ASP Chi-restraints excluded: chain A residue 1183 LEU Chi-restraints excluded: chain A residue 1232 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 379 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 5 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 34 optimal weight: 0.6980 chunk 59 optimal weight: 0.0970 chunk 42 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.120115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.095668 restraints weight = 14211.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.098463 restraints weight = 7895.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.100311 restraints weight = 5469.163| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 6548 Z= 0.203 Angle : 0.643 12.891 8830 Z= 0.326 Chirality : 0.044 0.216 959 Planarity : 0.003 0.049 1140 Dihedral : 4.850 45.867 882 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.30 % Allowed : 25.72 % Favored : 71.98 % 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: -0.96 (0.30), residues: 782 helix: 0.62 (0.27), residues: 378 sheet: -1.66 (0.40), residues: 139 loop : -1.79 (0.35), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1159 HIS 0.013 0.001 HIS B 387 PHE 0.010 0.001 PHE B 178 TYR 0.022 0.001 TYR A1214 ARG 0.002 0.000 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.763 Fit side-chains revert: symmetry clash REVERT: A 322 ASP cc_start: 0.7391 (p0) cc_final: 0.6325 (p0) REVERT: A 382 PHE cc_start: 0.8881 (OUTLIER) cc_final: 0.8381 (m-80) REVERT: A 413 HIS cc_start: 0.8219 (t-90) cc_final: 0.7762 (t-90) REVERT: A 1094 ASP cc_start: 0.8158 (m-30) cc_final: 0.7905 (m-30) REVERT: A 1157 MET cc_start: 0.7259 (tpp) cc_final: 0.6800 (ttm) REVERT: B 125 GLN cc_start: 0.7695 (tp40) cc_final: 0.7450 (pt0) outliers start: 16 outliers final: 13 residues processed: 119 average time/residue: 0.1641 time to fit residues: 27.3079 Evaluate side-chains 116 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 1095 GLU Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1110 THR Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1151 ASP Chi-restraints excluded: chain A residue 1232 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 379 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 55 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 491 HIS B 98 ASN B 170 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.118641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.094093 restraints weight = 14461.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.096917 restraints weight = 7897.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.098764 restraints weight = 5430.371| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 6548 Z= 0.258 Angle : 0.682 13.325 8830 Z= 0.345 Chirality : 0.045 0.258 959 Planarity : 0.003 0.050 1140 Dihedral : 4.934 45.882 882 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.73 % Allowed : 25.29 % Favored : 71.98 % 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: -1.06 (0.29), residues: 782 helix: 0.47 (0.27), residues: 378 sheet: -1.77 (0.40), residues: 135 loop : -1.69 (0.35), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1159 HIS 0.012 0.001 HIS B 387 PHE 0.028 0.001 PHE B 376 TYR 0.018 0.001 TYR A1214 ARG 0.003 0.000 ARG A1084 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 322 ASP cc_start: 0.7361 (p0) cc_final: 0.6448 (p0) REVERT: A 382 PHE cc_start: 0.8896 (OUTLIER) cc_final: 0.8407 (m-80) REVERT: A 413 HIS cc_start: 0.8172 (t-90) cc_final: 0.7720 (t-90) REVERT: A 1094 ASP cc_start: 0.8145 (m-30) cc_final: 0.7896 (m-30) REVERT: A 1157 MET cc_start: 0.7314 (tpp) cc_final: 0.6815 (ttm) REVERT: B 125 GLN cc_start: 0.7646 (tp40) cc_final: 0.7424 (pt0) REVERT: B 142 PHE cc_start: 0.7395 (m-80) cc_final: 0.7164 (m-80) outliers start: 19 outliers final: 18 residues processed: 122 average time/residue: 0.1595 time to fit residues: 27.3575 Evaluate side-chains 118 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 464 GLU Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 1036 ILE Chi-restraints excluded: chain A residue 1050 THR Chi-restraints excluded: chain A residue 1095 GLU Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1110 THR Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1151 ASP Chi-restraints excluded: chain A residue 1232 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 379 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 3 optimal weight: 5.9990 chunk 11 optimal weight: 0.4980 chunk 1 optimal weight: 1.9990 chunk 72 optimal weight: 0.0870 chunk 67 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 43 optimal weight: 0.0270 chunk 41 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 overall best weight: 0.5016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1208 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.121112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.096275 restraints weight = 14352.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.099199 restraints weight = 7779.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.101102 restraints weight = 5328.959| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 6548 Z= 0.204 Angle : 0.677 13.275 8830 Z= 0.340 Chirality : 0.045 0.305 959 Planarity : 0.003 0.051 1140 Dihedral : 4.902 46.017 882 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.30 % Allowed : 26.01 % Favored : 71.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.29), residues: 782 helix: 0.60 (0.27), residues: 374 sheet: -1.69 (0.39), residues: 135 loop : -1.61 (0.35), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1159 HIS 0.013 0.001 HIS B 387 PHE 0.009 0.001 PHE B 140 TYR 0.018 0.001 TYR A1214 ARG 0.003 0.000 ARG B 127 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2221.95 seconds wall clock time: 39 minutes 24.97 seconds (2364.97 seconds total)