Starting phenix.real_space_refine on Sat Jul 26 19:01:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nfj_49367/07_2025/9nfj_49367.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nfj_49367/07_2025/9nfj_49367.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9nfj_49367/07_2025/9nfj_49367.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nfj_49367/07_2025/9nfj_49367.map" model { file = "/net/cci-nas-00/data/ceres_data/9nfj_49367/07_2025/9nfj_49367.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nfj_49367/07_2025/9nfj_49367.cif" } resolution = 3.98 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= 0.047 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 49 5.16 5 C 5574 2.51 5 N 1474 2.21 5 O 1601 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 8698 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 8698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1122, 8698 Classifications: {'peptide': 1122} Link IDs: {'PTRANS': 32, 'TRANS': 1089} Chain breaks: 5 Time building chain proxies: 5.48, per 1000 atoms: 0.63 Number of scatterers: 8698 At special positions: 0 Unit cell: (76.67, 102.85, 143.99, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 49 16.00 O 1601 8.00 N 1474 7.00 C 5574 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: 2.90 Conformation dependent library (CDL) restraints added in 1.3 seconds 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2074 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 5 sheets defined 67.3% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 47 through 52 removed outlier: 4.008A pdb=" N PHE A 52 " --> pdb=" O PRO A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 96 removed outlier: 3.525A pdb=" N ALA A 72 " --> pdb=" O VAL A 68 " (cutoff:3.500A) Proline residue: A 78 - end of helix removed outlier: 3.524A pdb=" N MET A 96 " --> pdb=" O ILE A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 170 Processing helix chain 'A' and resid 171 through 178 Processing helix chain 'A' and resid 179 through 223 removed outlier: 4.068A pdb=" N VAL A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 239 Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 254 through 272 removed outlier: 3.610A pdb=" N ALA A 272 " --> pdb=" O GLU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 279 Processing helix chain 'A' and resid 281 through 336 Processing helix chain 'A' and resid 339 through 382 Proline residue: A 362 - end of helix removed outlier: 4.339A pdb=" N ILE A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 453 removed outlier: 3.750A pdb=" N THR A 448 " --> pdb=" O GLY A 444 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE A 449 " --> pdb=" O LYS A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 481 Processing helix chain 'A' and resid 496 through 502 Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 544 through 559 removed outlier: 4.151A pdb=" N ARG A 559 " --> pdb=" O ARG A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 590 removed outlier: 3.757A pdb=" N LEU A 590 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 604 removed outlier: 3.522A pdb=" N THR A 603 " --> pdb=" O ARG A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 630 Processing helix chain 'A' and resid 632 through 638 Processing helix chain 'A' and resid 714 through 721 removed outlier: 3.700A pdb=" N LEU A 721 " --> pdb=" O LYS A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 757 Proline residue: A 744 - end of helix Processing helix chain 'A' and resid 761 through 816 Processing helix chain 'A' and resid 818 through 826 Proline residue: A 824 - end of helix Processing helix chain 'A' and resid 827 through 870 Processing helix chain 'A' and resid 873 through 882 Processing helix chain 'A' and resid 882 through 891 removed outlier: 4.238A pdb=" N ALA A 886 " --> pdb=" O VAL A 882 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL A 887 " --> pdb=" O PRO A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 920 Processing helix chain 'A' and resid 920 through 927 Processing helix chain 'A' and resid 929 through 984 removed outlier: 4.465A pdb=" N VAL A 943 " --> pdb=" O GLU A 939 " (cutoff:3.500A) Proline residue: A 944 - end of helix Processing helix chain 'A' and resid 987 through 1001 removed outlier: 3.676A pdb=" N VAL A 991 " --> pdb=" O ASP A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1029 Processing helix chain 'A' and resid 1092 through 1101 removed outlier: 4.016A pdb=" N THR A1096 " --> pdb=" O GLY A1092 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE A1097 " --> pdb=" O LYS A1093 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1129 Processing helix chain 'A' and resid 1143 through 1150 Processing helix chain 'A' and resid 1158 through 1167 Processing helix chain 'A' and resid 1168 through 1170 No H-bonds generated for 'chain 'A' and resid 1168 through 1170' Processing helix chain 'A' and resid 1173 through 1177 Processing helix chain 'A' and resid 1194 through 1208 Processing helix chain 'A' and resid 1227 through 1239 Processing helix chain 'A' and resid 1273 through 1281 Processing helix chain 'A' and resid 1282 through 1288 Processing sheet with id=AA1, first strand: chain 'A' and resid 422 through 429 removed outlier: 5.180A pdb=" N ILE A 409 " --> pdb=" O ASN A 424 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N SER A 426 " --> pdb=" O ARG A 407 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ARG A 407 " --> pdb=" O SER A 426 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N SER A 428 " --> pdb=" O GLU A 405 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N GLU A 405 " --> pdb=" O SER A 428 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 482 through 485 removed outlier: 3.522A pdb=" N ASP A 567 " --> pdb=" O VAL A 485 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N LEU A 564 " --> pdb=" O ILE A 595 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N VAL A 597 " --> pdb=" O LEU A 564 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU A 566 " --> pdb=" O VAL A 597 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 494 through 495 Processing sheet with id=AA4, first strand: chain 'A' and resid 1064 through 1077 removed outlier: 7.281A pdb=" N TYR A1061 " --> pdb=" O PRO A1068 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N VAL A1057 " --> pdb=" O GLY A1072 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ASN A1074 " --> pdb=" O GLU A1055 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N GLU A1055 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LYS A1076 " --> pdb=" O ARG A1053 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ARG A1053 " --> pdb=" O LYS A1076 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1131 through 1133 removed outlier: 5.776A pdb=" N GLY A1131 " --> pdb=" O LEU A1215 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ASP A1217 " --> pdb=" O GLY A1131 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N VAL A1133 " --> pdb=" O ASP A1217 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N LEU A1214 " --> pdb=" O ILE A1245 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N VAL A1247 " --> pdb=" O LEU A1214 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU A1216 " --> pdb=" O VAL A1247 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU A1083 " --> pdb=" O CYS A1244 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N VAL A1246 " --> pdb=" O LEU A1083 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU A1270 " --> pdb=" O VAL A1262 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLN A1264 " --> pdb=" O VAL A1268 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N VAL A1268 " --> pdb=" O GLN A1264 " (cutoff:3.500A) 597 hydrogen bonds defined for protein. 1752 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: 4.18 Time building geometry restraints manager: 3.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2825 1.34 - 1.46: 1968 1.46 - 1.58: 3972 1.58 - 1.70: 0 1.70 - 1.82: 89 Bond restraints: 8854 Sorted by residual: bond pdb=" CB TRP A 979 " pdb=" CG TRP A 979 " ideal model delta sigma weight residual 1.498 1.543 -0.045 3.10e-02 1.04e+03 2.09e+00 bond pdb=" C LEU A1178 " pdb=" N PRO A1179 " ideal model delta sigma weight residual 1.334 1.365 -0.031 2.34e-02 1.83e+03 1.80e+00 bond pdb=" CA LEU A 77 " pdb=" C LEU A 77 " ideal model delta sigma weight residual 1.520 1.537 -0.016 1.23e-02 6.61e+03 1.78e+00 bond pdb=" CA ASN A1210 " pdb=" CB ASN A1210 " ideal model delta sigma weight residual 1.525 1.535 -0.010 8.30e-03 1.45e+04 1.44e+00 bond pdb=" C HIS A 73 " pdb=" O HIS A 73 " ideal model delta sigma weight residual 1.236 1.250 -0.014 1.15e-02 7.56e+03 1.40e+00 ... (remaining 8849 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 11811 2.48 - 4.95: 126 4.95 - 7.43: 16 7.43 - 9.91: 2 9.91 - 12.38: 3 Bond angle restraints: 11958 Sorted by residual: angle pdb=" CB MET A 729 " pdb=" CG MET A 729 " pdb=" SD MET A 729 " ideal model delta sigma weight residual 112.70 125.08 -12.38 3.00e+00 1.11e-01 1.70e+01 angle pdb=" CB MET A 481 " pdb=" CG MET A 481 " pdb=" SD MET A 481 " ideal model delta sigma weight residual 112.70 123.36 -10.66 3.00e+00 1.11e-01 1.26e+01 angle pdb=" CA MET A1020 " pdb=" CB MET A1020 " pdb=" CG MET A1020 " ideal model delta sigma weight residual 114.10 120.72 -6.62 2.00e+00 2.50e-01 1.10e+01 angle pdb=" CA LEU A 320 " pdb=" CB LEU A 320 " pdb=" CG LEU A 320 " ideal model delta sigma weight residual 116.30 127.69 -11.39 3.50e+00 8.16e-02 1.06e+01 angle pdb=" CB MET A1020 " pdb=" CG MET A1020 " pdb=" SD MET A1020 " ideal model delta sigma weight residual 112.70 122.39 -9.69 3.00e+00 1.11e-01 1.04e+01 ... (remaining 11953 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 4469 17.98 - 35.96: 621 35.96 - 53.94: 177 53.94 - 71.92: 25 71.92 - 89.90: 18 Dihedral angle restraints: 5310 sinusoidal: 2087 harmonic: 3223 Sorted by residual: dihedral pdb=" CA LEU A 999 " pdb=" C LEU A 999 " pdb=" N PHE A1000 " pdb=" CA PHE A1000 " ideal model delta harmonic sigma weight residual 180.00 161.63 18.37 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CB GLU A 121 " pdb=" CG GLU A 121 " pdb=" CD GLU A 121 " pdb=" OE1 GLU A 121 " ideal model delta sinusoidal sigma weight residual 0.00 89.90 -89.90 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU A 267 " pdb=" CG GLU A 267 " pdb=" CD GLU A 267 " pdb=" OE1 GLU A 267 " ideal model delta sinusoidal sigma weight residual 0.00 -89.86 89.86 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 5307 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1228 0.066 - 0.131: 142 0.131 - 0.197: 3 0.197 - 0.263: 0 0.263 - 0.329: 2 Chirality restraints: 1375 Sorted by residual: chirality pdb=" CG LEU A 320 " pdb=" CB LEU A 320 " pdb=" CD1 LEU A 320 " pdb=" CD2 LEU A 320 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.70e+00 chirality pdb=" CB ILE A 217 " pdb=" CA ILE A 217 " pdb=" CG1 ILE A 217 " pdb=" CG2 ILE A 217 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CB VAL A 869 " pdb=" CA VAL A 869 " pdb=" CG1 VAL A 869 " pdb=" CG2 VAL A 869 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 6.82e-01 ... (remaining 1372 not shown) Planarity restraints: 1522 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 198 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.82e+00 pdb=" C ILE A 198 " 0.045 2.00e-02 2.50e+03 pdb=" O ILE A 198 " -0.017 2.00e-02 2.50e+03 pdb=" N GLY A 199 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 979 " 0.014 2.00e-02 2.50e+03 1.44e-02 5.18e+00 pdb=" CG TRP A 979 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP A 979 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP A 979 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 979 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 979 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 979 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 979 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 979 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 979 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 77 " -0.035 5.00e-02 4.00e+02 5.39e-02 4.64e+00 pdb=" N PRO A 78 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 78 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 78 " -0.030 5.00e-02 4.00e+02 ... (remaining 1519 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 156 2.67 - 3.23: 9139 3.23 - 3.78: 14263 3.78 - 4.34: 17572 4.34 - 4.90: 28632 Nonbonded interactions: 69762 Sorted by model distance: nonbonded pdb=" O GLY A 444 " pdb=" OG1 THR A 447 " model vdw 2.111 3.040 nonbonded pdb=" OG1 THR A 494 " pdb=" OE2 GLU A 498 " model vdw 2.167 3.040 nonbonded pdb=" O TRP A 820 " pdb=" ND2 ASN A 826 " model vdw 2.187 3.120 nonbonded pdb=" OG1 THR A1158 " pdb=" OE1 GLU A1160 " model vdw 2.225 3.040 nonbonded pdb=" OD2 ASP A 56 " pdb=" NH2 ARG A 154 " model vdw 2.236 3.120 ... (remaining 69757 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 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: 0.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.990 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8854 Z= 0.152 Angle : 0.661 12.383 11958 Z= 0.346 Chirality : 0.042 0.329 1375 Planarity : 0.004 0.054 1522 Dihedral : 18.282 89.898 3236 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.01 % Allowed : 28.49 % Favored : 68.49 % 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: 0.93 (0.25), residues: 1110 helix: 1.53 (0.19), residues: 703 sheet: -0.71 (0.64), residues: 68 loop : -0.98 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 979 HIS 0.005 0.001 HIS A 375 PHE 0.035 0.002 PHE A 976 TYR 0.017 0.001 TYR A 259 ARG 0.002 0.000 ARG A 559 Details of bonding type rmsd hydrogen bonds : bond 0.11099 ( 597) hydrogen bonds : angle 5.35979 ( 1752) covalent geometry : bond 0.00309 ( 8854) covalent geometry : angle 0.66080 (11958) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 138 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 ASP cc_start: 0.7546 (OUTLIER) cc_final: 0.7321 (p0) REVERT: A 80 MET cc_start: 0.7131 (tmm) cc_final: 0.6434 (tmm) REVERT: A 123 MET cc_start: 0.8506 (tpt) cc_final: 0.8049 (tpt) REVERT: A 138 LEU cc_start: 0.9516 (OUTLIER) cc_final: 0.9265 (tt) REVERT: A 308 ASN cc_start: 0.8722 (m-40) cc_final: 0.8353 (t0) REVERT: A 475 VAL cc_start: 0.8766 (m) cc_final: 0.8419 (t) REVERT: A 533 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8000 (tm-30) REVERT: A 624 HIS cc_start: 0.8508 (OUTLIER) cc_final: 0.7770 (t-170) REVERT: A 729 MET cc_start: 0.7500 (mmm) cc_final: 0.7236 (mmm) REVERT: A 741 MET cc_start: 0.7628 (tpp) cc_final: 0.7189 (tpp) REVERT: A 945 TYR cc_start: 0.7172 (t80) cc_final: 0.6603 (t80) REVERT: A 965 MET cc_start: 0.7971 (mmm) cc_final: 0.7555 (mmp) REVERT: A 970 TYR cc_start: 0.7921 (OUTLIER) cc_final: 0.7265 (t80) REVERT: A 1027 MET cc_start: 0.6631 (ppp) cc_final: 0.6326 (ppp) REVERT: A 1136 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7609 (tm-30) REVERT: A 1207 ILE cc_start: 0.7739 (mm) cc_final: 0.7456 (mm) outliers start: 28 outliers final: 23 residues processed: 159 average time/residue: 0.1747 time to fit residues: 40.9156 Evaluate side-chains 161 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 133 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 613 PHE Chi-restraints excluded: chain A residue 624 HIS Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 746 PHE Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 757 PHE Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 970 TYR Chi-restraints excluded: chain A residue 1037 ASN Chi-restraints excluded: chain A residue 1061 TYR Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1096 THR Chi-restraints excluded: chain A residue 1114 ASP Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1182 TYR Chi-restraints excluded: chain A residue 1273 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 8.9990 chunk 84 optimal weight: 0.0570 chunk 47 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 45 optimal weight: 0.1980 chunk 87 optimal weight: 0.9990 chunk 33 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 overall best weight: 0.6102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1037 ASN ** A1108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.136178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.112881 restraints weight = 19249.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.115871 restraints weight = 11224.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.117856 restraints weight = 7768.551| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.0688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8854 Z= 0.137 Angle : 0.568 7.009 11958 Z= 0.301 Chirality : 0.041 0.237 1375 Planarity : 0.004 0.055 1522 Dihedral : 7.213 53.252 1249 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 4.30 % Allowed : 25.91 % Favored : 69.78 % 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: 1.10 (0.25), residues: 1110 helix: 1.63 (0.19), residues: 715 sheet: -0.69 (0.64), residues: 68 loop : -0.93 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 979 HIS 0.004 0.001 HIS A 375 PHE 0.023 0.001 PHE A1000 TYR 0.018 0.001 TYR A 259 ARG 0.003 0.000 ARG A 600 Details of bonding type rmsd hydrogen bonds : bond 0.05022 ( 597) hydrogen bonds : angle 4.84418 ( 1752) covalent geometry : bond 0.00269 ( 8854) covalent geometry : angle 0.56835 (11958) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 144 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.6593 (tmm) cc_final: 0.6207 (tmm) REVERT: A 123 MET cc_start: 0.8737 (tpt) cc_final: 0.8155 (tpt) REVERT: A 135 PHE cc_start: 0.8587 (m-80) cc_final: 0.8260 (m-10) REVERT: A 138 LEU cc_start: 0.9448 (OUTLIER) cc_final: 0.9216 (tt) REVERT: A 311 MET cc_start: 0.7160 (tpp) cc_final: 0.6806 (tpp) REVERT: A 349 VAL cc_start: 0.9144 (m) cc_final: 0.8653 (p) REVERT: A 475 VAL cc_start: 0.8859 (m) cc_final: 0.8539 (t) REVERT: A 604 ILE cc_start: 0.8295 (OUTLIER) cc_final: 0.7962 (tt) REVERT: A 624 HIS cc_start: 0.8473 (OUTLIER) cc_final: 0.8012 (t-170) REVERT: A 741 MET cc_start: 0.7574 (tpp) cc_final: 0.7253 (tpp) REVERT: A 868 PHE cc_start: 0.7023 (OUTLIER) cc_final: 0.6784 (t80) REVERT: A 874 LEU cc_start: 0.7856 (mt) cc_final: 0.7552 (mt) REVERT: A 945 TYR cc_start: 0.7046 (t80) cc_final: 0.6463 (t80) REVERT: A 965 MET cc_start: 0.7954 (mmm) cc_final: 0.7679 (mmp) REVERT: A 970 TYR cc_start: 0.7918 (OUTLIER) cc_final: 0.7345 (t80) REVERT: A 976 PHE cc_start: 0.7968 (t80) cc_final: 0.7408 (t80) REVERT: A 980 LEU cc_start: 0.8649 (mt) cc_final: 0.8047 (tt) REVERT: A 1071 ARG cc_start: 0.6072 (mtm180) cc_final: 0.5506 (ptt-90) REVERT: A 1136 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7573 (tm-30) outliers start: 40 outliers final: 23 residues processed: 172 average time/residue: 0.1927 time to fit residues: 50.1803 Evaluate side-chains 164 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 136 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 613 PHE Chi-restraints excluded: chain A residue 624 HIS Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 746 PHE Chi-restraints excluded: chain A residue 757 PHE Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain A residue 868 PHE Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 882 VAL Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 970 TYR Chi-restraints excluded: chain A residue 1061 TYR Chi-restraints excluded: chain A residue 1182 TYR Chi-restraints excluded: chain A residue 1273 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 18 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 89 optimal weight: 0.0980 chunk 41 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 overall best weight: 1.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1030 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.132033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.108322 restraints weight = 19094.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.111345 restraints weight = 10851.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.113354 restraints weight = 7386.763| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.0945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8854 Z= 0.154 Angle : 0.584 7.583 11958 Z= 0.306 Chirality : 0.041 0.277 1375 Planarity : 0.004 0.061 1522 Dihedral : 6.140 52.057 1224 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 5.91 % Allowed : 25.05 % Favored : 69.03 % 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: 1.13 (0.25), residues: 1110 helix: 1.66 (0.19), residues: 715 sheet: -0.96 (0.60), residues: 73 loop : -0.86 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 979 HIS 0.008 0.001 HIS A1108 PHE 0.023 0.001 PHE A1000 TYR 0.018 0.001 TYR A 259 ARG 0.002 0.000 ARG A 288 Details of bonding type rmsd hydrogen bonds : bond 0.05014 ( 597) hydrogen bonds : angle 4.75127 ( 1752) covalent geometry : bond 0.00319 ( 8854) covalent geometry : angle 0.58362 (11958) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 145 time to evaluate : 1.037 Fit side-chains revert: symmetry clash REVERT: A 123 MET cc_start: 0.8864 (tpt) cc_final: 0.8342 (mmm) REVERT: A 135 PHE cc_start: 0.8729 (m-80) cc_final: 0.8427 (m-10) REVERT: A 138 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8703 (tt) REVERT: A 299 MET cc_start: 0.7861 (mmt) cc_final: 0.7470 (mmt) REVERT: A 311 MET cc_start: 0.7210 (tpp) cc_final: 0.6837 (tpp) REVERT: A 595 ILE cc_start: 0.9635 (OUTLIER) cc_final: 0.9388 (mm) REVERT: A 604 ILE cc_start: 0.8561 (OUTLIER) cc_final: 0.8197 (tt) REVERT: A 624 HIS cc_start: 0.8498 (OUTLIER) cc_final: 0.8023 (t-170) REVERT: A 874 LEU cc_start: 0.7992 (mt) cc_final: 0.7685 (mt) REVERT: A 945 TYR cc_start: 0.7204 (t80) cc_final: 0.6634 (t80) REVERT: A 970 TYR cc_start: 0.8121 (OUTLIER) cc_final: 0.7396 (t80) REVERT: A 976 PHE cc_start: 0.8111 (t80) cc_final: 0.7454 (t80) REVERT: A 1071 ARG cc_start: 0.6256 (mtm180) cc_final: 0.5719 (ptt-90) REVERT: A 1136 GLU cc_start: 0.7996 (tm-30) cc_final: 0.7613 (tm-30) outliers start: 55 outliers final: 30 residues processed: 190 average time/residue: 0.1670 time to fit residues: 46.8920 Evaluate side-chains 174 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 139 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 624 HIS Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 746 PHE Chi-restraints excluded: chain A residue 757 PHE Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 816 GLN Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 850 MET Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain A residue 868 PHE Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 970 TYR Chi-restraints excluded: chain A residue 1031 ARG Chi-restraints excluded: chain A residue 1061 TYR Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1182 TYR Chi-restraints excluded: chain A residue 1230 VAL Chi-restraints excluded: chain A residue 1273 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 77 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 97 optimal weight: 0.4980 chunk 17 optimal weight: 8.9990 chunk 31 optimal weight: 6.9990 chunk 98 optimal weight: 0.6980 chunk 90 optimal weight: 10.0000 chunk 105 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.132911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.109156 restraints weight = 18940.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.112164 restraints weight = 10800.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.114270 restraints weight = 7373.096| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8854 Z= 0.138 Angle : 0.585 7.963 11958 Z= 0.302 Chirality : 0.040 0.203 1375 Planarity : 0.004 0.058 1522 Dihedral : 5.884 50.856 1221 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 4.73 % Allowed : 26.67 % Favored : 68.60 % 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: 1.20 (0.25), residues: 1110 helix: 1.71 (0.19), residues: 713 sheet: -0.79 (0.63), residues: 68 loop : -0.84 (0.34), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 979 HIS 0.004 0.001 HIS A 375 PHE 0.035 0.001 PHE A 974 TYR 0.018 0.001 TYR A 259 ARG 0.002 0.000 ARG A 605 Details of bonding type rmsd hydrogen bonds : bond 0.04826 ( 597) hydrogen bonds : angle 4.69440 ( 1752) covalent geometry : bond 0.00286 ( 8854) covalent geometry : angle 0.58470 (11958) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 144 time to evaluate : 1.016 Fit side-chains revert: symmetry clash REVERT: A 123 MET cc_start: 0.8492 (tpt) cc_final: 0.8223 (mmm) REVERT: A 135 PHE cc_start: 0.8715 (m-80) cc_final: 0.8331 (m-10) REVERT: A 138 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8677 (tt) REVERT: A 162 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8282 (mp) REVERT: A 299 MET cc_start: 0.7914 (mmt) cc_final: 0.7560 (mmt) REVERT: A 311 MET cc_start: 0.7173 (tpp) cc_final: 0.6877 (tpp) REVERT: A 604 ILE cc_start: 0.8550 (OUTLIER) cc_final: 0.8189 (tt) REVERT: A 624 HIS cc_start: 0.8490 (OUTLIER) cc_final: 0.8033 (t-170) REVERT: A 874 LEU cc_start: 0.7983 (mt) cc_final: 0.7677 (mt) REVERT: A 945 TYR cc_start: 0.7148 (t80) cc_final: 0.6583 (t80) REVERT: A 970 TYR cc_start: 0.8115 (OUTLIER) cc_final: 0.7396 (t80) REVERT: A 976 PHE cc_start: 0.8084 (t80) cc_final: 0.7543 (t80) REVERT: A 980 LEU cc_start: 0.8665 (mt) cc_final: 0.8005 (tt) REVERT: A 1032 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8108 (pm20) REVERT: A 1064 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7902 (ptp90) REVERT: A 1071 ARG cc_start: 0.5960 (mtm180) cc_final: 0.5565 (ptt-90) REVERT: A 1136 GLU cc_start: 0.7979 (tm-30) cc_final: 0.7596 (tm-30) outliers start: 44 outliers final: 27 residues processed: 178 average time/residue: 0.1697 time to fit residues: 44.1498 Evaluate side-chains 170 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 136 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 613 PHE Chi-restraints excluded: chain A residue 624 HIS Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 746 PHE Chi-restraints excluded: chain A residue 757 PHE Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 850 MET Chi-restraints excluded: chain A residue 868 PHE Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 882 VAL Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 970 TYR Chi-restraints excluded: chain A residue 1031 ARG Chi-restraints excluded: chain A residue 1032 GLU Chi-restraints excluded: chain A residue 1061 TYR Chi-restraints excluded: chain A residue 1064 ARG Chi-restraints excluded: chain A residue 1182 TYR Chi-restraints excluded: chain A residue 1273 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 91 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 111 optimal weight: 7.9990 chunk 7 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 48 optimal weight: 0.0000 chunk 82 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.132227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.108253 restraints weight = 18877.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.111267 restraints weight = 10874.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.113276 restraints weight = 7464.690| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8854 Z= 0.151 Angle : 0.587 9.582 11958 Z= 0.305 Chirality : 0.042 0.331 1375 Planarity : 0.004 0.057 1522 Dihedral : 5.812 51.921 1219 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 6.02 % Allowed : 25.91 % Favored : 68.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.25), residues: 1110 helix: 1.72 (0.19), residues: 715 sheet: -0.98 (0.60), residues: 73 loop : -0.82 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 979 HIS 0.004 0.001 HIS A 375 PHE 0.050 0.001 PHE A 974 TYR 0.018 0.001 TYR A 259 ARG 0.002 0.000 ARG A 605 Details of bonding type rmsd hydrogen bonds : bond 0.04841 ( 597) hydrogen bonds : angle 4.69038 ( 1752) covalent geometry : bond 0.00320 ( 8854) covalent geometry : angle 0.58704 (11958) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 137 time to evaluate : 1.133 Fit side-chains revert: symmetry clash REVERT: A 138 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8626 (tt) REVERT: A 162 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8261 (mp) REVERT: A 299 MET cc_start: 0.7938 (mmt) cc_final: 0.7567 (mmt) REVERT: A 311 MET cc_start: 0.7257 (tpp) cc_final: 0.6911 (tpp) REVERT: A 315 PHE cc_start: 0.8678 (m-80) cc_final: 0.7961 (m-80) REVERT: A 347 PHE cc_start: 0.8127 (t80) cc_final: 0.7746 (t80) REVERT: A 595 ILE cc_start: 0.9620 (OUTLIER) cc_final: 0.9364 (mm) REVERT: A 604 ILE cc_start: 0.8518 (OUTLIER) cc_final: 0.8207 (tt) REVERT: A 624 HIS cc_start: 0.8506 (OUTLIER) cc_final: 0.8041 (t-170) REVERT: A 945 TYR cc_start: 0.7610 (t80) cc_final: 0.7070 (t80) REVERT: A 970 TYR cc_start: 0.7934 (OUTLIER) cc_final: 0.7364 (t80) REVERT: A 980 LEU cc_start: 0.8692 (mt) cc_final: 0.8028 (tt) REVERT: A 1032 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8104 (pm20) REVERT: A 1064 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7914 (ptp90) REVERT: A 1071 ARG cc_start: 0.6111 (mtm180) cc_final: 0.5695 (ptt-90) REVERT: A 1136 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7621 (tm-30) outliers start: 56 outliers final: 34 residues processed: 184 average time/residue: 0.1877 time to fit residues: 52.7214 Evaluate side-chains 176 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 134 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 624 HIS Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 746 PHE Chi-restraints excluded: chain A residue 757 PHE Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 816 GLN Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 850 MET Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain A residue 868 PHE Chi-restraints excluded: chain A residue 882 VAL Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 970 TYR Chi-restraints excluded: chain A residue 995 ILE Chi-restraints excluded: chain A residue 1031 ARG Chi-restraints excluded: chain A residue 1032 GLU Chi-restraints excluded: chain A residue 1061 TYR Chi-restraints excluded: chain A residue 1064 ARG Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1157 VAL Chi-restraints excluded: chain A residue 1182 TYR Chi-restraints excluded: chain A residue 1230 VAL Chi-restraints excluded: chain A residue 1273 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 69 optimal weight: 0.8980 chunk 105 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 71 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 308 ASN ** 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 = 0.3886 r_free = 0.3886 target = 0.131548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.107871 restraints weight = 18734.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.110827 restraints weight = 10783.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.112877 restraints weight = 7387.229| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8854 Z= 0.174 Angle : 0.631 10.149 11958 Z= 0.323 Chirality : 0.042 0.218 1375 Planarity : 0.004 0.057 1522 Dihedral : 5.725 53.031 1217 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 5.27 % Allowed : 27.20 % Favored : 67.53 % 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: 1.17 (0.25), residues: 1110 helix: 1.72 (0.19), residues: 708 sheet: -1.01 (0.66), residues: 63 loop : -0.87 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 979 HIS 0.004 0.001 HIS A 375 PHE 0.059 0.002 PHE A 974 TYR 0.018 0.002 TYR A 259 ARG 0.003 0.000 ARG A 288 Details of bonding type rmsd hydrogen bonds : bond 0.04979 ( 597) hydrogen bonds : angle 4.71448 ( 1752) covalent geometry : bond 0.00373 ( 8854) covalent geometry : angle 0.63085 (11958) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 136 time to evaluate : 0.999 Fit side-chains REVERT: A 138 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8652 (tt) REVERT: A 162 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8254 (mp) REVERT: A 216 PHE cc_start: 0.7487 (m-80) cc_final: 0.6984 (t80) REVERT: A 299 MET cc_start: 0.7954 (mmt) cc_final: 0.7571 (mmt) REVERT: A 347 PHE cc_start: 0.8230 (t80) cc_final: 0.7875 (t80) REVERT: A 595 ILE cc_start: 0.9567 (OUTLIER) cc_final: 0.9339 (mm) REVERT: A 624 HIS cc_start: 0.8503 (OUTLIER) cc_final: 0.7725 (t-170) REVERT: A 741 MET cc_start: 0.7997 (tpp) cc_final: 0.7741 (tpp) REVERT: A 945 TYR cc_start: 0.7652 (t80) cc_final: 0.7155 (t80) REVERT: A 970 TYR cc_start: 0.8063 (OUTLIER) cc_final: 0.7414 (t80) REVERT: A 1032 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8113 (pm20) REVERT: A 1064 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7902 (ptp90) REVERT: A 1071 ARG cc_start: 0.6201 (mtm180) cc_final: 0.5815 (ptt-90) REVERT: A 1136 GLU cc_start: 0.8009 (tm-30) cc_final: 0.7630 (tm-30) outliers start: 49 outliers final: 32 residues processed: 175 average time/residue: 0.1846 time to fit residues: 48.5635 Evaluate side-chains 172 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 133 time to evaluate : 1.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 613 PHE Chi-restraints excluded: chain A residue 624 HIS Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 757 PHE Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 776 PHE Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 816 GLN Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 850 MET Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain A residue 868 PHE Chi-restraints excluded: chain A residue 882 VAL Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 970 TYR Chi-restraints excluded: chain A residue 995 ILE Chi-restraints excluded: chain A residue 1031 ARG Chi-restraints excluded: chain A residue 1032 GLU Chi-restraints excluded: chain A residue 1061 TYR Chi-restraints excluded: chain A residue 1064 ARG Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1157 VAL Chi-restraints excluded: chain A residue 1182 TYR Chi-restraints excluded: chain A residue 1230 VAL Chi-restraints excluded: chain A residue 1273 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 9 optimal weight: 1.9990 chunk 70 optimal weight: 0.0970 chunk 97 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 102 optimal weight: 9.9990 chunk 68 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 72 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.132532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.108881 restraints weight = 18810.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.111907 restraints weight = 10806.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.113948 restraints weight = 7377.066| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8854 Z= 0.143 Angle : 0.623 12.265 11958 Z= 0.312 Chirality : 0.042 0.374 1375 Planarity : 0.004 0.054 1522 Dihedral : 5.608 54.514 1215 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 4.84 % Allowed : 27.85 % Favored : 67.31 % 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: 1.23 (0.25), residues: 1110 helix: 1.76 (0.19), residues: 716 sheet: -1.09 (0.66), residues: 63 loop : -0.88 (0.34), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 979 HIS 0.004 0.001 HIS A 375 PHE 0.021 0.001 PHE A1000 TYR 0.019 0.001 TYR A 259 ARG 0.002 0.000 ARG A 288 Details of bonding type rmsd hydrogen bonds : bond 0.04835 ( 597) hydrogen bonds : angle 4.63263 ( 1752) covalent geometry : bond 0.00300 ( 8854) covalent geometry : angle 0.62258 (11958) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 138 time to evaluate : 1.037 Fit side-chains REVERT: A 138 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8655 (tt) REVERT: A 162 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8245 (mp) REVERT: A 299 MET cc_start: 0.7830 (mmt) cc_final: 0.7435 (mmt) REVERT: A 311 MET cc_start: 0.7398 (tpp) cc_final: 0.7094 (tmm) REVERT: A 315 PHE cc_start: 0.8633 (m-80) cc_final: 0.8044 (m-80) REVERT: A 347 PHE cc_start: 0.8192 (t80) cc_final: 0.7835 (t80) REVERT: A 595 ILE cc_start: 0.9601 (OUTLIER) cc_final: 0.9333 (mm) REVERT: A 604 ILE cc_start: 0.8489 (OUTLIER) cc_final: 0.8145 (tt) REVERT: A 624 HIS cc_start: 0.8478 (OUTLIER) cc_final: 0.7962 (t-170) REVERT: A 741 MET cc_start: 0.8014 (tpp) cc_final: 0.7713 (tpp) REVERT: A 874 LEU cc_start: 0.8363 (mt) cc_final: 0.7244 (tp) REVERT: A 945 TYR cc_start: 0.7578 (t80) cc_final: 0.7087 (t80) REVERT: A 970 TYR cc_start: 0.7852 (OUTLIER) cc_final: 0.7258 (t80) REVERT: A 1032 GLU cc_start: 0.8879 (OUTLIER) cc_final: 0.8208 (pm20) REVERT: A 1064 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7895 (ptp90) REVERT: A 1071 ARG cc_start: 0.6280 (mtm180) cc_final: 0.6046 (ptt-90) REVERT: A 1136 GLU cc_start: 0.7997 (tm-30) cc_final: 0.7633 (tm-30) REVERT: A 1207 ILE cc_start: 0.8631 (mm) cc_final: 0.8088 (mt) outliers start: 45 outliers final: 30 residues processed: 174 average time/residue: 0.1654 time to fit residues: 42.8386 Evaluate side-chains 171 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 133 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 624 HIS Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 757 PHE Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 776 PHE Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 816 GLN Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 850 MET Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain A residue 868 PHE Chi-restraints excluded: chain A residue 882 VAL Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 970 TYR Chi-restraints excluded: chain A residue 1031 ARG Chi-restraints excluded: chain A residue 1032 GLU Chi-restraints excluded: chain A residue 1061 TYR Chi-restraints excluded: chain A residue 1064 ARG Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1157 VAL Chi-restraints excluded: chain A residue 1182 TYR Chi-restraints excluded: chain A residue 1273 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 25 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 94 optimal weight: 0.0170 chunk 82 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.6822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.133458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.109878 restraints weight = 18975.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.112935 restraints weight = 10814.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.114975 restraints weight = 7338.478| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8854 Z= 0.135 Angle : 0.656 15.917 11958 Z= 0.319 Chirality : 0.043 0.331 1375 Planarity : 0.004 0.054 1522 Dihedral : 5.607 55.936 1215 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 4.73 % Allowed : 28.28 % Favored : 66.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.25), residues: 1110 helix: 1.82 (0.19), residues: 716 sheet: -1.12 (0.65), residues: 63 loop : -0.84 (0.34), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 979 HIS 0.004 0.001 HIS A 375 PHE 0.018 0.001 PHE A1000 TYR 0.017 0.001 TYR A 259 ARG 0.002 0.000 ARG A 288 Details of bonding type rmsd hydrogen bonds : bond 0.04737 ( 597) hydrogen bonds : angle 4.58439 ( 1752) covalent geometry : bond 0.00277 ( 8854) covalent geometry : angle 0.65616 (11958) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 139 time to evaluate : 0.996 Fit side-chains REVERT: A 138 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8568 (tt) REVERT: A 162 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8261 (mp) REVERT: A 299 MET cc_start: 0.7848 (mmt) cc_final: 0.7471 (mmt) REVERT: A 311 MET cc_start: 0.7399 (tpp) cc_final: 0.7152 (tpp) REVERT: A 347 PHE cc_start: 0.8110 (t80) cc_final: 0.7719 (t80) REVERT: A 471 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.7271 (mpt-90) REVERT: A 488 GLU cc_start: 0.8968 (tm-30) cc_final: 0.8670 (tm-30) REVERT: A 595 ILE cc_start: 0.9590 (OUTLIER) cc_final: 0.9334 (mm) REVERT: A 604 ILE cc_start: 0.8487 (OUTLIER) cc_final: 0.8141 (tt) REVERT: A 624 HIS cc_start: 0.8449 (OUTLIER) cc_final: 0.7974 (t-170) REVERT: A 741 MET cc_start: 0.7993 (tpp) cc_final: 0.7713 (tpp) REVERT: A 874 LEU cc_start: 0.8329 (mt) cc_final: 0.7200 (tp) REVERT: A 945 TYR cc_start: 0.7125 (t80) cc_final: 0.6595 (t80) REVERT: A 970 TYR cc_start: 0.7872 (OUTLIER) cc_final: 0.7226 (t80) REVERT: A 1032 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.8310 (pm20) REVERT: A 1064 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7880 (ptp90) REVERT: A 1071 ARG cc_start: 0.6216 (mtm180) cc_final: 0.6006 (ptt-90) REVERT: A 1136 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7612 (tm-30) REVERT: A 1207 ILE cc_start: 0.8631 (mm) cc_final: 0.8096 (mt) outliers start: 44 outliers final: 28 residues processed: 177 average time/residue: 0.2139 time to fit residues: 55.2795 Evaluate side-chains 172 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 135 time to evaluate : 1.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 471 ARG Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 613 PHE Chi-restraints excluded: chain A residue 624 HIS Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 757 PHE Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 816 GLN Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 850 MET Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain A residue 868 PHE Chi-restraints excluded: chain A residue 882 VAL Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 970 TYR Chi-restraints excluded: chain A residue 1031 ARG Chi-restraints excluded: chain A residue 1032 GLU Chi-restraints excluded: chain A residue 1061 TYR Chi-restraints excluded: chain A residue 1064 ARG Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1157 VAL Chi-restraints excluded: chain A residue 1182 TYR Chi-restraints excluded: chain A residue 1230 VAL Chi-restraints excluded: chain A residue 1273 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 33 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 76 optimal weight: 0.7980 chunk 55 optimal weight: 5.9990 chunk 12 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 82 optimal weight: 0.0870 chunk 61 optimal weight: 0.0010 chunk 102 optimal weight: 0.0570 chunk 107 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.3282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.136640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.112291 restraints weight = 18788.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.115414 restraints weight = 10803.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.117569 restraints weight = 7426.459| |-----------------------------------------------------------------------------| r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8854 Z= 0.132 Angle : 0.661 15.562 11958 Z= 0.320 Chirality : 0.043 0.306 1375 Planarity : 0.004 0.053 1522 Dihedral : 5.579 57.840 1215 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.87 % Allowed : 29.03 % Favored : 67.10 % 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: 1.34 (0.25), residues: 1110 helix: 1.85 (0.19), residues: 714 sheet: -0.93 (0.68), residues: 58 loop : -0.85 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 979 HIS 0.004 0.001 HIS A 375 PHE 0.017 0.001 PHE A1000 TYR 0.019 0.001 TYR A 322 ARG 0.002 0.000 ARG A 559 Details of bonding type rmsd hydrogen bonds : bond 0.04543 ( 597) hydrogen bonds : angle 4.51738 ( 1752) covalent geometry : bond 0.00263 ( 8854) covalent geometry : angle 0.66090 (11958) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 139 time to evaluate : 2.113 Fit side-chains revert: symmetry clash REVERT: A 138 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8535 (tt) REVERT: A 162 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8177 (mp) REVERT: A 204 MET cc_start: 0.8338 (mmm) cc_final: 0.8121 (mmp) REVERT: A 299 MET cc_start: 0.7890 (mmt) cc_final: 0.7484 (mmt) REVERT: A 311 MET cc_start: 0.7302 (tpp) cc_final: 0.7019 (tmm) REVERT: A 315 PHE cc_start: 0.8613 (m-80) cc_final: 0.8018 (m-80) REVERT: A 320 LEU cc_start: 0.8776 (mm) cc_final: 0.8355 (tt) REVERT: A 347 PHE cc_start: 0.7827 (t80) cc_final: 0.7464 (t80) REVERT: A 471 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.7293 (mpt-90) REVERT: A 488 GLU cc_start: 0.8964 (tm-30) cc_final: 0.8278 (tm-30) REVERT: A 595 ILE cc_start: 0.9583 (OUTLIER) cc_final: 0.9331 (mm) REVERT: A 624 HIS cc_start: 0.8419 (OUTLIER) cc_final: 0.7715 (t-170) REVERT: A 874 LEU cc_start: 0.8403 (mt) cc_final: 0.7259 (tp) REVERT: A 945 TYR cc_start: 0.6971 (t80) cc_final: 0.6499 (t80) REVERT: A 970 TYR cc_start: 0.7732 (OUTLIER) cc_final: 0.7152 (t80) REVERT: A 1032 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8308 (mp0) REVERT: A 1064 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7855 (ptp90) REVERT: A 1071 ARG cc_start: 0.6053 (mtm180) cc_final: 0.5845 (ptt-90) REVERT: A 1136 GLU cc_start: 0.7950 (tm-30) cc_final: 0.7589 (tm-30) REVERT: A 1185 GLN cc_start: 0.7718 (mp10) cc_final: 0.7002 (tm-30) REVERT: A 1207 ILE cc_start: 0.8328 (mm) cc_final: 0.7643 (mt) outliers start: 36 outliers final: 24 residues processed: 169 average time/residue: 0.2219 time to fit residues: 54.0330 Evaluate side-chains 167 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 135 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 471 ARG Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 624 HIS Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 746 PHE Chi-restraints excluded: chain A residue 757 PHE Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 850 MET Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain A residue 868 PHE Chi-restraints excluded: chain A residue 882 VAL Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 970 TYR Chi-restraints excluded: chain A residue 1031 ARG Chi-restraints excluded: chain A residue 1032 GLU Chi-restraints excluded: chain A residue 1061 TYR Chi-restraints excluded: chain A residue 1064 ARG Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1157 VAL Chi-restraints excluded: chain A residue 1182 TYR Chi-restraints excluded: chain A residue 1230 VAL Chi-restraints excluded: chain A residue 1273 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 110 optimal weight: 8.9990 chunk 13 optimal weight: 0.6980 chunk 71 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 chunk 108 optimal weight: 0.6980 chunk 105 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 chunk 43 optimal weight: 6.9990 chunk 14 optimal weight: 0.7980 chunk 78 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.135907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.111590 restraints weight = 19083.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.114687 restraints weight = 11020.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.116829 restraints weight = 7592.743| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8854 Z= 0.133 Angle : 0.673 16.088 11958 Z= 0.324 Chirality : 0.042 0.301 1375 Planarity : 0.004 0.054 1522 Dihedral : 5.556 59.405 1215 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.33 % Allowed : 29.68 % Favored : 66.99 % 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: 1.38 (0.25), residues: 1110 helix: 1.88 (0.19), residues: 715 sheet: -0.87 (0.68), residues: 57 loop : -0.85 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 979 HIS 0.004 0.001 HIS A 375 PHE 0.018 0.001 PHE A1000 TYR 0.016 0.001 TYR A 322 ARG 0.002 0.000 ARG A 605 Details of bonding type rmsd hydrogen bonds : bond 0.04536 ( 597) hydrogen bonds : angle 4.50461 ( 1752) covalent geometry : bond 0.00277 ( 8854) covalent geometry : angle 0.67305 (11958) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 132 time to evaluate : 1.037 Fit side-chains revert: symmetry clash REVERT: A 138 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8558 (tt) REVERT: A 162 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8270 (mp) REVERT: A 204 MET cc_start: 0.8359 (mmm) cc_final: 0.8125 (mmp) REVERT: A 299 MET cc_start: 0.7909 (mmt) cc_final: 0.7484 (mmt) REVERT: A 311 MET cc_start: 0.7335 (tpp) cc_final: 0.7078 (tmm) REVERT: A 315 PHE cc_start: 0.8632 (m-80) cc_final: 0.8059 (m-80) REVERT: A 320 LEU cc_start: 0.8559 (mm) cc_final: 0.7992 (tt) REVERT: A 347 PHE cc_start: 0.7854 (t80) cc_final: 0.7443 (t80) REVERT: A 471 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7407 (mpt-90) REVERT: A 488 GLU cc_start: 0.9041 (tm-30) cc_final: 0.8396 (tm-30) REVERT: A 595 ILE cc_start: 0.9593 (OUTLIER) cc_final: 0.9346 (mm) REVERT: A 741 MET cc_start: 0.7977 (tpp) cc_final: 0.7704 (tpp) REVERT: A 874 LEU cc_start: 0.8415 (mt) cc_final: 0.7295 (tp) REVERT: A 945 TYR cc_start: 0.7035 (t80) cc_final: 0.6497 (t80) REVERT: A 970 TYR cc_start: 0.7762 (OUTLIER) cc_final: 0.7142 (t80) REVERT: A 1032 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.8319 (mp0) REVERT: A 1064 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7868 (ptp90) REVERT: A 1071 ARG cc_start: 0.6078 (mtm180) cc_final: 0.5870 (ptt-90) REVERT: A 1136 GLU cc_start: 0.7994 (tm-30) cc_final: 0.7623 (tm-30) REVERT: A 1207 ILE cc_start: 0.8336 (mm) cc_final: 0.7652 (mt) outliers start: 31 outliers final: 23 residues processed: 157 average time/residue: 0.1804 time to fit residues: 41.4291 Evaluate side-chains 162 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 132 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 471 ARG Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 757 PHE Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 850 MET Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain A residue 868 PHE Chi-restraints excluded: chain A residue 882 VAL Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 970 TYR Chi-restraints excluded: chain A residue 1031 ARG Chi-restraints excluded: chain A residue 1032 GLU Chi-restraints excluded: chain A residue 1061 TYR Chi-restraints excluded: chain A residue 1064 ARG Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1157 VAL Chi-restraints excluded: chain A residue 1182 TYR Chi-restraints excluded: chain A residue 1230 VAL Chi-restraints excluded: chain A residue 1273 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 111 optimal weight: 6.9990 chunk 57 optimal weight: 0.0670 chunk 69 optimal weight: 3.9990 chunk 61 optimal weight: 0.1980 chunk 26 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 chunk 46 optimal weight: 10.0000 chunk 42 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.136382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.112057 restraints weight = 19133.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.115151 restraints weight = 11070.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.117328 restraints weight = 7623.815| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8854 Z= 0.131 Angle : 0.674 16.158 11958 Z= 0.325 Chirality : 0.042 0.275 1375 Planarity : 0.004 0.054 1522 Dihedral : 5.420 59.458 1213 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.55 % Allowed : 29.46 % Favored : 66.99 % 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: 1.37 (0.25), residues: 1110 helix: 1.87 (0.19), residues: 715 sheet: -0.87 (0.68), residues: 57 loop : -0.86 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 979 HIS 0.004 0.000 HIS A 375 PHE 0.018 0.001 PHE A1000 TYR 0.023 0.001 TYR A 322 ARG 0.002 0.000 ARG A 559 Details of bonding type rmsd hydrogen bonds : bond 0.04511 ( 597) hydrogen bonds : angle 4.49566 ( 1752) covalent geometry : bond 0.00270 ( 8854) covalent geometry : angle 0.67421 (11958) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3048.57 seconds wall clock time: 57 minutes 8.28 seconds (3428.28 seconds total)