Starting phenix.real_space_refine on Tue Feb 13 15:16:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r4p_4722/02_2024/6r4p_4722_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r4p_4722/02_2024/6r4p_4722.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r4p_4722/02_2024/6r4p_4722.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r4p_4722/02_2024/6r4p_4722.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r4p_4722/02_2024/6r4p_4722_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r4p_4722/02_2024/6r4p_4722_updated.pdb" } resolution = 3.1 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= 0.003 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 4149 2.51 5 N 1139 2.21 5 O 1245 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 340": "NH1" <-> "NH2" Residue "A ARG 383": "NH1" <-> "NH2" Residue "A ARG 471": "NH1" <-> "NH2" Residue "A ARG 504": "NH1" <-> "NH2" Residue "A PHE 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1127": "NH1" <-> "NH2" Residue "A ARG 1148": "NH1" <-> "NH2" Residue "A ARG 1206": "NH1" <-> "NH2" Residue "A PHE 1224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6583 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3741 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 12, 'TRANS': 465} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2842 Unusual residues: {' MG': 1, 'GSP': 1} Classifications: {'peptide': 341, 'undetermined': 2} Link IDs: {'PTRANS': 13, 'TRANS': 327, None: 2} Not linked: pdbres="GLN B 390 " pdbres="GSP B 501 " Not linked: pdbres="GSP B 501 " pdbres=" MG B 502 " Chain breaks: 1 Time building chain proxies: 4.09, per 1000 atoms: 0.62 Number of scatterers: 6583 At special positions: 0 Unit cell: (100.122, 106.634, 103.378, 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 1245 8.00 N 1139 7.00 C 4149 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.46 Conformation dependent library (CDL) restraints added in 1.3 seconds 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1540 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 31 helices and 7 sheets defined 43.2% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'A' and resid 321 through 335 Processing helix chain 'A' and resid 340 through 347 Processing helix chain 'A' and resid 352 through 358 Processing helix chain 'A' and resid 403 through 406 No H-bonds generated for 'chain 'A' and resid 403 through 406' Processing helix chain 'A' and resid 414 through 433 Processing helix chain 'A' and resid 458 through 480 Processing helix chain 'A' and resid 512 through 522 Processing helix chain 'A' and resid 533 through 536 No H-bonds generated for 'chain 'A' and resid 533 through 536' Processing helix chain 'A' and resid 1021 through 1036 Processing helix chain 'A' and resid 1039 through 1046 Processing helix chain 'A' and resid 1066 through 1071 removed outlier: 4.364A pdb=" N SER A1069 " --> pdb=" O VAL A1066 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU A1070 " --> pdb=" O ASN A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1080 through 1098 removed outlier: 3.769A pdb=" N LEU A1097 " --> pdb=" O PHE A1093 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N SER A1098 " --> pdb=" O ASP A1094 " (cutoff:3.500A) Processing helix chain 'A' and resid 1134 through 1155 removed outlier: 3.741A pdb=" N ASN A1155 " --> pdb=" O ASP A1151 " (cutoff:3.500A) Processing helix chain 'A' and resid 1190 through 1200 Processing helix chain 'A' and resid 1211 through 1220 removed outlier: 4.371A pdb=" N LYS A1219 " --> pdb=" O ARG A1215 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N MET A1220 " --> pdb=" O VAL A1216 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 39 Processing helix chain 'B' and resid 53 through 64 Processing helix chain 'B' and resid 90 through 112 removed outlier: 4.214A pdb=" N SER B 111 " --> pdb=" O VAL B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 133 removed outlier: 3.935A pdb=" N GLN B 125 " --> pdb=" O PRO B 122 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N PHE B 126 " --> pdb=" O GLU B 123 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU B 132 " --> pdb=" O ASP B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 154 Processing helix chain 'B' and resid 157 through 164 Processing helix chain 'B' and resid 175 through 184 removed outlier: 4.023A pdb=" N ASP B 180 " --> pdb=" O GLN B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 199 Processing helix chain 'B' and resid 228 through 233 removed outlier: 3.680A pdb=" N ARG B 231 " --> pdb=" O ARG B 228 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ARG B 232 " --> pdb=" O ASP B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 237 No H-bonds generated for 'chain 'B' and resid 235 through 237' Processing helix chain 'B' and resid 265 through 277 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 308 through 310 No H-bonds generated for 'chain 'B' and resid 308 through 310' Processing helix chain 'B' and resid 313 through 315 No H-bonds generated for 'chain 'B' and resid 313 through 315' Processing helix chain 'B' and resid 332 through 351 removed outlier: 3.872A pdb=" N ILE B 348 " --> pdb=" O GLU B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 388 Processing sheet with id= A, first strand: chain 'A' and resid 386 through 390 removed outlier: 4.321A pdb=" N LYS A 386 " --> pdb=" O ILE A 499 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 436 through 441 removed outlier: 7.531A pdb=" N TYR A 446 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N THR A 440 " --> pdb=" O CYS A 444 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N CYS A 444 " --> pdb=" O THR A 440 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN A 485 " --> pdb=" O VAL A 401 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 1052 through 1055 Processing sheet with id= D, first strand: chain 'A' and resid 1060 through 1065 Processing sheet with id= E, first strand: chain 'A' and resid 1105 through 1111 removed outlier: 7.134A pdb=" N MET A1116 " --> pdb=" O ILE A1108 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N THR A1110 " --> pdb=" O THR A1114 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N THR A1114 " --> pdb=" O THR A1110 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1225 through 1232 removed outlier: 7.179A pdb=" N THR A1240 " --> pdb=" O ARG A1227 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N THR A1229 " --> pdb=" O MET A1238 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N MET A1238 " --> pdb=" O THR A1229 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ASN A1231 " --> pdb=" O GLY A1236 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N GLY A1236 " --> pdb=" O ASN A1231 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 359 through 363 removed outlier: 7.570A pdb=" N VAL B 287 " --> pdb=" O TYR B 360 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N HIS B 362 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU B 289 " --> pdb=" O HIS B 362 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ILE B 244 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N PHE B 290 " --> pdb=" O ILE B 244 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N PHE B 246 " --> pdb=" O PHE B 290 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ASN B 292 " --> pdb=" O PHE B 246 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N VAL B 248 " --> pdb=" O ASN B 292 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N VAL B 224 " --> pdb=" O LEU B 45 " (cutoff:3.500A) 294 hydrogen bonds defined for protein. 822 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: 2.13 Time building geometry restraints manager: 2.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1983 1.33 - 1.45: 1059 1.45 - 1.57: 3586 1.57 - 1.69: 5 1.69 - 1.81: 72 Bond restraints: 6705 Sorted by residual: bond pdb=" CB VAL A1041 " pdb=" CG1 VAL A1041 " ideal model delta sigma weight residual 1.521 1.446 0.075 3.30e-02 9.18e+02 5.22e+00 bond pdb=" CG LEU A1139 " pdb=" CD1 LEU A1139 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.77e+00 bond pdb=" CB VAL A1166 " pdb=" CG2 VAL A1166 " ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.66e+00 bond pdb=" CD LYS A1107 " pdb=" CE LYS A1107 " ideal model delta sigma weight residual 1.520 1.463 0.057 3.00e-02 1.11e+03 3.59e+00 bond pdb=" CG LEU A1164 " pdb=" CD2 LEU A1164 " ideal model delta sigma weight residual 1.521 1.462 0.059 3.30e-02 9.18e+02 3.22e+00 ... (remaining 6700 not shown) Histogram of bond angle deviations from ideal: 97.70 - 105.07: 104 105.07 - 112.44: 3243 112.44 - 119.80: 2536 119.80 - 127.17: 3099 127.17 - 134.54: 63 Bond angle restraints: 9045 Sorted by residual: angle pdb=" C ASN B 239 " pdb=" N ASP B 240 " pdb=" CA ASP B 240 " ideal model delta sigma weight residual 121.54 131.67 -10.13 1.91e+00 2.74e-01 2.81e+01 angle pdb=" C THR A1180 " pdb=" N THR A1181 " pdb=" CA THR A1181 " ideal model delta sigma weight residual 121.54 131.17 -9.63 1.91e+00 2.74e-01 2.54e+01 angle pdb=" C VAL B 214 " pdb=" N ASP B 215 " pdb=" CA ASP B 215 " ideal model delta sigma weight residual 121.54 130.61 -9.07 1.91e+00 2.74e-01 2.25e+01 angle pdb=" CA CYS A 451 " pdb=" CB CYS A 451 " pdb=" SG CYS A 451 " ideal model delta sigma weight residual 114.40 124.15 -9.75 2.30e+00 1.89e-01 1.80e+01 angle pdb=" CB MET A 469 " pdb=" CG MET A 469 " pdb=" SD MET A 469 " ideal model delta sigma weight residual 112.70 100.03 12.67 3.00e+00 1.11e-01 1.78e+01 ... (remaining 9040 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.46: 3754 15.46 - 30.91: 210 30.91 - 46.37: 76 46.37 - 61.82: 6 61.82 - 77.28: 8 Dihedral angle restraints: 4054 sinusoidal: 1669 harmonic: 2385 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 180.00 144.60 35.40 0 5.00e+00 4.00e-02 5.01e+01 dihedral pdb=" CA TYR A1072 " pdb=" C TYR A1072 " pdb=" N GLU A1073 " pdb=" CA GLU A1073 " ideal model delta harmonic sigma weight residual -180.00 -145.07 -34.93 0 5.00e+00 4.00e-02 4.88e+01 dihedral pdb=" CA ILE B 182 " pdb=" C ILE B 182 " pdb=" N ASP B 183 " pdb=" CA ASP B 183 " ideal model delta harmonic sigma weight residual 180.00 152.35 27.65 0 5.00e+00 4.00e-02 3.06e+01 ... (remaining 4051 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 764 0.071 - 0.141: 197 0.141 - 0.211: 17 0.211 - 0.282: 6 0.282 - 0.352: 2 Chirality restraints: 986 Sorted by residual: chirality pdb=" CB ILE B 185 " pdb=" CA ILE B 185 " pdb=" CG1 ILE B 185 " pdb=" CG2 ILE B 185 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" CB ILE A1061 " pdb=" CA ILE A1061 " pdb=" CG1 ILE A1061 " pdb=" CG2 ILE A1061 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CA TYR A1243 " pdb=" N TYR A1243 " pdb=" C TYR A1243 " pdb=" CB TYR A1243 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.50e+00 ... (remaining 983 not shown) Planarity restraints: 1170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 114 " -0.052 5.00e-02 4.00e+02 7.80e-02 9.73e+00 pdb=" N PRO B 115 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO B 115 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 115 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A1087 " 0.014 2.00e-02 2.50e+03 2.82e-02 7.98e+00 pdb=" CG ASN A1087 " -0.049 2.00e-02 2.50e+03 pdb=" OD1 ASN A1087 " 0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN A1087 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A1037 " 0.045 5.00e-02 4.00e+02 6.84e-02 7.49e+00 pdb=" N PRO A1038 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO A1038 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A1038 " 0.037 5.00e-02 4.00e+02 ... (remaining 1167 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 80 2.64 - 3.21: 5807 3.21 - 3.77: 10269 3.77 - 4.34: 14044 4.34 - 4.90: 22745 Nonbonded interactions: 52945 Sorted by model distance: nonbonded pdb=" O2B GSP B 501 " pdb="MG MG B 502 " model vdw 2.080 2.170 nonbonded pdb=" OG SER B 54 " pdb="MG MG B 502 " model vdw 2.121 2.170 nonbonded pdb=" O2G GSP B 501 " pdb="MG MG B 502 " model vdw 2.129 2.170 nonbonded pdb=" OG1 THR B 204 " pdb="MG MG B 502 " model vdw 2.132 2.170 nonbonded pdb=" O ALA A 412 " pdb=" OG SER A1052 " model vdw 2.210 2.440 ... (remaining 52940 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: 1.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 5.680 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 22.630 Find NCS groups from input model: 0.170 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 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 0.075 6705 Z= 0.543 Angle : 1.043 12.673 9045 Z= 0.552 Chirality : 0.063 0.352 986 Planarity : 0.007 0.078 1170 Dihedral : 11.941 77.280 2514 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 0.57 % Allowed : 6.51 % Favored : 92.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.13 % 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: -3.18 (0.25), residues: 807 helix: -1.99 (0.21), residues: 356 sheet: -1.76 (0.41), residues: 143 loop : -2.18 (0.32), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.004 TRP A1159 HIS 0.015 0.003 HIS B 149 PHE 0.042 0.004 PHE A 397 TYR 0.036 0.003 TYR A 446 ARG 0.015 0.001 ARG B 342 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 89 time to evaluate : 0.780 Fit side-chains revert: symmetry clash REVERT: A 333 MET cc_start: 0.8845 (mmt) cc_final: 0.8507 (mmp) REVERT: A 1220 MET cc_start: 0.8294 (mtm) cc_final: 0.8080 (mtp) outliers start: 4 outliers final: 0 residues processed: 93 average time/residue: 0.2800 time to fit residues: 32.2872 Evaluate side-chains 51 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 68 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 20 optimal weight: 0.3980 chunk 41 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 GLN ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1154 ASN A1193 ASN A1231 ASN B 98 ASN B 213 GLN B 239 ASN B 264 ASN B 362 HIS B 371 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6705 Z= 0.193 Angle : 0.583 7.744 9045 Z= 0.305 Chirality : 0.044 0.169 986 Planarity : 0.004 0.060 1170 Dihedral : 5.437 32.551 908 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.70 % Allowed : 9.05 % Favored : 89.25 % 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: -1.59 (0.28), residues: 807 helix: -0.24 (0.26), residues: 361 sheet: -1.16 (0.41), residues: 137 loop : -1.87 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1159 HIS 0.003 0.001 HIS B 149 PHE 0.013 0.001 PHE A1093 TYR 0.019 0.002 TYR A 446 ARG 0.004 0.000 ARG A1215 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 57 time to evaluate : 0.823 Fit side-chains revert: symmetry clash REVERT: A 465 MET cc_start: 0.8778 (tmt) cc_final: 0.7986 (tmt) REVERT: A 1027 ASP cc_start: 0.7812 (OUTLIER) cc_final: 0.7497 (m-30) REVERT: A 1158 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8835 (pp) outliers start: 12 outliers final: 2 residues processed: 66 average time/residue: 0.1964 time to fit residues: 17.8552 Evaluate side-chains 51 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 47 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain B residue 171 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 40 optimal weight: 0.0010 chunk 22 optimal weight: 0.0270 chunk 61 optimal weight: 0.0370 chunk 50 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 59 optimal weight: 0.0020 chunk 72 optimal weight: 5.9990 overall best weight: 0.1330 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6705 Z= 0.125 Angle : 0.513 7.575 9045 Z= 0.266 Chirality : 0.042 0.155 986 Planarity : 0.003 0.056 1170 Dihedral : 4.712 27.053 908 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.84 % Allowed : 10.89 % Favored : 87.27 % 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: -0.67 (0.29), residues: 807 helix: 0.66 (0.27), residues: 360 sheet: -0.71 (0.41), residues: 134 loop : -1.57 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1159 HIS 0.004 0.001 HIS A 530 PHE 0.010 0.001 PHE A 505 TYR 0.017 0.001 TYR A 446 ARG 0.004 0.000 ARG B 374 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 63 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 465 MET cc_start: 0.8715 (tmt) cc_final: 0.7922 (tmt) REVERT: A 1047 VAL cc_start: 0.8591 (m) cc_final: 0.8367 (p) REVERT: A 1157 MET cc_start: 0.8598 (tpp) cc_final: 0.8289 (mmm) REVERT: A 1158 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8684 (pp) REVERT: B 188 ASP cc_start: 0.7611 (p0) cc_final: 0.7220 (t0) outliers start: 13 outliers final: 1 residues processed: 72 average time/residue: 0.1683 time to fit residues: 17.2467 Evaluate side-chains 51 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 49 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain B residue 171 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 55 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 73 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 65 optimal weight: 0.4980 chunk 44 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6705 Z= 0.193 Angle : 0.537 7.625 9045 Z= 0.277 Chirality : 0.043 0.182 986 Planarity : 0.003 0.054 1170 Dihedral : 4.625 29.576 908 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.70 % Allowed : 12.87 % Favored : 85.43 % 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: -0.25 (0.29), residues: 807 helix: 0.96 (0.27), residues: 361 sheet: 0.07 (0.43), residues: 125 loop : -1.57 (0.34), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1159 HIS 0.006 0.001 HIS B 357 PHE 0.013 0.001 PHE A 385 TYR 0.018 0.001 TYR A 446 ARG 0.003 0.000 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 48 time to evaluate : 0.761 Fit side-chains revert: symmetry clash REVERT: A 1027 ASP cc_start: 0.7791 (OUTLIER) cc_final: 0.7409 (m-30) REVERT: A 1047 VAL cc_start: 0.8583 (m) cc_final: 0.8368 (p) REVERT: A 1157 MET cc_start: 0.8679 (tpp) cc_final: 0.8354 (mmm) REVERT: A 1158 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8738 (pp) REVERT: B 188 ASP cc_start: 0.7624 (p0) cc_final: 0.7226 (t0) REVERT: B 213 GLN cc_start: 0.8036 (OUTLIER) cc_final: 0.7769 (tm-30) outliers start: 12 outliers final: 4 residues processed: 59 average time/residue: 0.1977 time to fit residues: 16.3452 Evaluate side-chains 51 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 44 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1174 THR Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 213 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 1 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 0 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6705 Z= 0.200 Angle : 0.535 7.565 9045 Z= 0.275 Chirality : 0.043 0.154 986 Planarity : 0.003 0.055 1170 Dihedral : 4.561 29.716 908 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.40 % Allowed : 13.15 % Favored : 84.44 % 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: -0.07 (0.29), residues: 807 helix: 1.13 (0.27), residues: 361 sheet: 0.01 (0.44), residues: 121 loop : -1.41 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1159 HIS 0.006 0.001 HIS B 357 PHE 0.014 0.001 PHE B 212 TYR 0.018 0.001 TYR A 446 ARG 0.003 0.000 ARG B 374 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 48 time to evaluate : 0.898 Fit side-chains REVERT: A 465 MET cc_start: 0.9060 (OUTLIER) cc_final: 0.8144 (tmt) REVERT: A 1027 ASP cc_start: 0.7797 (OUTLIER) cc_final: 0.7414 (m-30) REVERT: A 1047 VAL cc_start: 0.8580 (m) cc_final: 0.8361 (p) REVERT: A 1157 MET cc_start: 0.8689 (tpp) cc_final: 0.8389 (mmm) REVERT: A 1158 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8762 (pp) REVERT: B 188 ASP cc_start: 0.7680 (p0) cc_final: 0.7251 (t0) outliers start: 17 outliers final: 7 residues processed: 63 average time/residue: 0.1667 time to fit residues: 15.0938 Evaluate side-chains 56 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 46 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 1027 ASP Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain A residue 1174 THR Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 184 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 45 optimal weight: 0.0770 chunk 19 optimal weight: 0.0770 chunk 78 optimal weight: 4.9990 chunk 65 optimal weight: 0.0770 chunk 36 optimal weight: 0.9980 chunk 6 optimal weight: 0.0870 chunk 25 optimal weight: 0.0070 chunk 41 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 overall best weight: 0.0650 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6705 Z= 0.110 Angle : 0.487 7.871 9045 Z= 0.248 Chirality : 0.041 0.139 986 Planarity : 0.003 0.055 1170 Dihedral : 4.149 23.375 908 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.70 % Allowed : 12.87 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.30), residues: 807 helix: 1.55 (0.28), residues: 357 sheet: 0.51 (0.44), residues: 123 loop : -1.19 (0.35), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1159 HIS 0.003 0.001 HIS B 357 PHE 0.014 0.001 PHE B 212 TYR 0.015 0.001 TYR A 446 ARG 0.005 0.000 ARG A1165 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 59 time to evaluate : 0.881 Fit side-chains revert: symmetry clash REVERT: A 465 MET cc_start: 0.8923 (OUTLIER) cc_final: 0.8088 (tmt) REVERT: A 1157 MET cc_start: 0.8538 (tpp) cc_final: 0.8202 (mmm) REVERT: B 188 ASP cc_start: 0.7599 (p0) cc_final: 0.7246 (t0) outliers start: 12 outliers final: 5 residues processed: 68 average time/residue: 0.1662 time to fit residues: 15.9638 Evaluate side-chains 59 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 53 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 ASN Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 1150 VAL Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 221 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 57 optimal weight: 8.9990 chunk 44 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 78 optimal weight: 0.2980 chunk 48 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 HIS ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6705 Z= 0.234 Angle : 0.545 8.560 9045 Z= 0.278 Chirality : 0.043 0.158 986 Planarity : 0.003 0.052 1170 Dihedral : 4.341 29.269 908 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.56 % Allowed : 14.00 % Favored : 84.44 % 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: 0.38 (0.30), residues: 807 helix: 1.51 (0.27), residues: 360 sheet: 0.39 (0.45), residues: 120 loop : -1.25 (0.35), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1159 HIS 0.006 0.001 HIS B 357 PHE 0.014 0.002 PHE A1093 TYR 0.017 0.001 TYR A 446 ARG 0.003 0.000 ARG A1165 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 48 time to evaluate : 0.825 Fit side-chains REVERT: A 465 MET cc_start: 0.9121 (OUTLIER) cc_final: 0.8197 (tmt) REVERT: A 1157 MET cc_start: 0.8698 (tpp) cc_final: 0.8133 (mmm) REVERT: B 188 ASP cc_start: 0.7633 (p0) cc_final: 0.7224 (t0) outliers start: 11 outliers final: 5 residues processed: 57 average time/residue: 0.1725 time to fit residues: 14.1257 Evaluate side-chains 50 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 44 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 184 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 15 optimal weight: 4.9990 chunk 49 optimal weight: 0.2980 chunk 53 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 61 optimal weight: 0.0170 chunk 71 optimal weight: 3.9990 chunk 74 optimal weight: 0.0270 chunk 68 optimal weight: 0.8980 chunk 72 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 overall best weight: 0.3676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6705 Z= 0.143 Angle : 0.518 10.996 9045 Z= 0.259 Chirality : 0.041 0.145 986 Planarity : 0.003 0.055 1170 Dihedral : 4.181 26.513 908 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.41 % Allowed : 14.43 % Favored : 84.16 % 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: 0.55 (0.30), residues: 807 helix: 1.59 (0.27), residues: 366 sheet: 0.72 (0.45), residues: 115 loop : -1.21 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1159 HIS 0.004 0.001 HIS B 357 PHE 0.010 0.001 PHE B 212 TYR 0.016 0.001 TYR A 446 ARG 0.002 0.000 ARG A1165 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 45 time to evaluate : 0.877 Fit side-chains REVERT: A 1147 MET cc_start: 0.8994 (tpp) cc_final: 0.8767 (mmm) REVERT: A 1157 MET cc_start: 0.8596 (tpp) cc_final: 0.8030 (mmm) REVERT: B 188 ASP cc_start: 0.7623 (p0) cc_final: 0.7231 (t0) outliers start: 10 outliers final: 5 residues processed: 53 average time/residue: 0.1818 time to fit residues: 13.9253 Evaluate side-chains 48 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 43 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 ASN Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain B residue 171 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 31 optimal weight: 0.8980 chunk 57 optimal weight: 9.9990 chunk 22 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 72 optimal weight: 0.0170 chunk 47 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 46 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6705 Z= 0.174 Angle : 0.516 7.926 9045 Z= 0.261 Chirality : 0.042 0.152 986 Planarity : 0.003 0.052 1170 Dihedral : 4.181 27.656 908 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.99 % Allowed : 15.13 % Favored : 83.88 % 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: 0.60 (0.30), residues: 807 helix: 1.58 (0.27), residues: 367 sheet: 0.79 (0.45), residues: 115 loop : -1.16 (0.35), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1159 HIS 0.005 0.001 HIS B 357 PHE 0.011 0.001 PHE B 212 TYR 0.016 0.001 TYR A 446 ARG 0.003 0.000 ARG A1165 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 41 time to evaluate : 0.847 Fit side-chains REVERT: A 1157 MET cc_start: 0.8619 (tpp) cc_final: 0.8016 (mmm) REVERT: B 188 ASP cc_start: 0.7625 (p0) cc_final: 0.7228 (t0) outliers start: 7 outliers final: 4 residues processed: 47 average time/residue: 0.1811 time to fit residues: 12.5519 Evaluate side-chains 45 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 41 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 ASN Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain B residue 171 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 80 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 6 optimal weight: 0.2980 chunk 49 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 6705 Z= 0.312 Angle : 0.619 12.543 9045 Z= 0.309 Chirality : 0.045 0.168 986 Planarity : 0.004 0.050 1170 Dihedral : 4.627 33.412 908 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.27 % Allowed : 15.13 % Favored : 83.59 % 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: 0.34 (0.30), residues: 807 helix: 1.39 (0.27), residues: 368 sheet: 0.51 (0.45), residues: 116 loop : -1.26 (0.35), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 234 HIS 0.008 0.001 HIS B 357 PHE 0.014 0.002 PHE B 222 TYR 0.020 0.002 TYR A 446 ARG 0.003 0.001 ARG A 425 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 43 time to evaluate : 0.778 Fit side-chains REVERT: A 1147 MET cc_start: 0.9051 (tpp) cc_final: 0.8804 (mmm) REVERT: A 1157 MET cc_start: 0.8691 (tpp) cc_final: 0.8032 (mmm) REVERT: B 188 ASP cc_start: 0.7670 (p0) cc_final: 0.7229 (t0) outliers start: 9 outliers final: 6 residues processed: 50 average time/residue: 0.1732 time to fit residues: 12.6204 Evaluate side-chains 48 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 42 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 409 ASN Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain B residue 171 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 17 optimal weight: 0.6980 chunk 64 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 66 optimal weight: 0.0270 chunk 8 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 56 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 73 optimal weight: 0.5980 chunk 43 optimal weight: 5.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.099135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.076547 restraints weight = 13743.566| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.70 r_work: 0.3023 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6705 Z= 0.166 Angle : 0.528 7.572 9045 Z= 0.268 Chirality : 0.042 0.148 986 Planarity : 0.003 0.051 1170 Dihedral : 4.361 28.723 908 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.85 % Allowed : 15.56 % Favored : 83.59 % 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: 0.50 (0.30), residues: 807 helix: 1.46 (0.27), residues: 370 sheet: 0.73 (0.45), residues: 115 loop : -1.17 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1159 HIS 0.005 0.001 HIS A 530 PHE 0.011 0.001 PHE B 212 TYR 0.017 0.001 TYR A 446 ARG 0.003 0.000 ARG B 385 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1763.07 seconds wall clock time: 33 minutes 38.16 seconds (2018.16 seconds total)