Starting phenix.real_space_refine on Wed Sep 17 13:03:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nfj_49367/09_2025/9nfj_49367.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nfj_49367/09_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_49367/09_2025/9nfj_49367.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nfj_49367/09_2025/9nfj_49367.map" model { file = "/net/cci-nas-00/data/ceres_data/9nfj_49367/09_2025/9nfj_49367.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nfj_49367/09_2025/9nfj_49367.cif" } resolution = 3.98 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.99, per 1000 atoms: 0.23 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: 1.01 Conformation dependent library (CDL) restraints added in 380.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.29 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: 1.43 Time building geometry restraints manager: 1.27 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: 0.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.540 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.170 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG A 559 TYR 0.017 0.001 TYR A 259 PHE 0.035 0.002 PHE A 976 TRP 0.038 0.002 TRP A 979 HIS 0.005 0.001 HIS A 375 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 8854) covalent geometry : angle 0.66080 (11958) hydrogen bonds : bond 0.11099 ( 597) hydrogen bonds : angle 5.35979 ( 1752) *********************** 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 : 0.337 Fit side-chains revert: symmetry clash 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: 0.8418 (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: 0.7771 (t-170) REVERT: A 729 MET cc_start: 0.7500 (mmm) cc_final: 0.7237 (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: 0.7553 (mmp) REVERT: A 970 TYR cc_start: 0.7921 (OUTLIER) cc_final: 0.7266 (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: 0.0771 time to fit residues: 18.5184 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 : 0.352 ------------------------------------------------------------------------------- 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 108 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.3980 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 10.0000 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1030 ASN A1037 ASN ** A1108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.133081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.109215 restraints weight = 19699.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.112064 restraints weight = 11589.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.114007 restraints weight = 8150.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.115293 restraints weight = 6435.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.116075 restraints weight = 5501.726| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.0719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8854 Z= 0.191 Angle : 0.611 7.150 11958 Z= 0.326 Chirality : 0.042 0.226 1375 Planarity : 0.004 0.061 1522 Dihedral : 7.362 53.172 1249 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 5.27 % Allowed : 26.24 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.25), residues: 1110 helix: 1.49 (0.19), residues: 709 sheet: -0.95 (0.60), residues: 73 loop : -0.96 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 288 TYR 0.017 0.002 TYR A 259 PHE 0.025 0.002 PHE A1000 TRP 0.021 0.002 TRP A 979 HIS 0.004 0.001 HIS A 375 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 8854) covalent geometry : angle 0.61073 (11958) hydrogen bonds : bond 0.05417 ( 597) hydrogen bonds : angle 5.01166 ( 1752) *********************** 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 191 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 142 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.8151 (tpt) cc_final: 0.7785 (tpt) REVERT: A 138 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8407 (tp) REVERT: A 308 ASN cc_start: 0.8590 (m-40) cc_final: 0.8288 (t0) REVERT: A 311 MET cc_start: 0.7182 (tpp) cc_final: 0.6830 (tpp) REVERT: A 475 VAL cc_start: 0.8796 (m) cc_final: 0.8461 (t) REVERT: A 604 ILE cc_start: 0.8282 (OUTLIER) cc_final: 0.7939 (tt) REVERT: A 624 HIS cc_start: 0.8501 (OUTLIER) cc_final: 0.7987 (t-170) REVERT: A 741 MET cc_start: 0.7637 (tpp) cc_final: 0.7338 (tpp) REVERT: A 874 LEU cc_start: 0.7934 (mt) cc_final: 0.7650 (mt) REVERT: A 945 TYR cc_start: 0.7626 (t80) cc_final: 0.7074 (t80) REVERT: A 965 MET cc_start: 0.8013 (mmm) cc_final: 0.7762 (mmp) REVERT: A 970 TYR cc_start: 0.8006 (OUTLIER) cc_final: 0.7370 (t80) REVERT: A 976 PHE cc_start: 0.7790 (t80) cc_final: 0.7151 (t80) REVERT: A 1114 ASP cc_start: 0.9381 (OUTLIER) cc_final: 0.8801 (m-30) REVERT: A 1136 GLU cc_start: 0.7941 (tm-30) cc_final: 0.7593 (tm-30) outliers start: 49 outliers final: 28 residues processed: 177 average time/residue: 0.0760 time to fit residues: 20.2628 Evaluate side-chains 171 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 138 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE 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 256 GLN Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 419 VAL 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 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 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 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 1100 LEU Chi-restraints excluded: chain A residue 1114 ASP Chi-restraints excluded: chain A residue 1159 LEU 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 103 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 73 optimal weight: 0.2980 chunk 56 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 111 optimal weight: 9.9990 chunk 37 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN A 410 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.135631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.112293 restraints weight = 19439.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.115238 restraints weight = 11505.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.117195 restraints weight = 8070.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.118340 restraints weight = 6366.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.119282 restraints weight = 5467.356| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.0895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8854 Z= 0.136 Angle : 0.576 7.216 11958 Z= 0.301 Chirality : 0.041 0.291 1375 Planarity : 0.004 0.058 1522 Dihedral : 6.085 51.876 1224 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 5.59 % Allowed : 25.81 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.25), residues: 1110 helix: 1.65 (0.19), residues: 715 sheet: -0.83 (0.63), residues: 68 loop : -0.90 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 288 TYR 0.019 0.001 TYR A 259 PHE 0.021 0.001 PHE A1000 TRP 0.015 0.001 TRP A 979 HIS 0.004 0.001 HIS A 375 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 8854) covalent geometry : angle 0.57606 (11958) hydrogen bonds : bond 0.04996 ( 597) hydrogen bonds : angle 4.74197 ( 1752) *********************** 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 201 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 149 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.8639 (tpt) cc_final: 0.8358 (tpp) REVERT: A 138 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8648 (tt) REVERT: A 162 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8306 (mp) REVERT: A 299 MET cc_start: 0.7779 (mmt) cc_final: 0.7390 (mmt) REVERT: A 311 MET cc_start: 0.7170 (tpp) cc_final: 0.6395 (tpp) REVERT: A 315 PHE cc_start: 0.8639 (m-80) cc_final: 0.7931 (m-80) REVERT: A 349 VAL cc_start: 0.9161 (m) cc_final: 0.8679 (p) REVERT: A 475 VAL cc_start: 0.8837 (m) cc_final: 0.8479 (t) REVERT: A 595 ILE cc_start: 0.9603 (OUTLIER) cc_final: 0.9373 (mm) REVERT: A 604 ILE cc_start: 0.8420 (OUTLIER) cc_final: 0.8073 (tt) REVERT: A 624 HIS cc_start: 0.8492 (OUTLIER) cc_final: 0.8024 (t-170) REVERT: A 741 MET cc_start: 0.7608 (tpp) cc_final: 0.7260 (tpp) REVERT: A 874 LEU cc_start: 0.7819 (mt) cc_final: 0.7468 (mt) REVERT: A 945 TYR cc_start: 0.7468 (t80) cc_final: 0.6976 (t80) REVERT: A 970 TYR cc_start: 0.7911 (OUTLIER) cc_final: 0.7329 (t80) REVERT: A 1032 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8063 (pm20) REVERT: A 1136 GLU cc_start: 0.7897 (tm-30) cc_final: 0.7549 (tm-30) outliers start: 52 outliers final: 28 residues processed: 190 average time/residue: 0.0783 time to fit residues: 22.1928 Evaluate side-chains 170 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 135 time to evaluate : 0.347 ------------------------------------------------------------------------------- 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 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 748 VAL 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 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 993 LEU 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 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 51 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 chunk 103 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 73 optimal weight: 0.2980 chunk 26 optimal weight: 0.1980 chunk 81 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3912 r_free = 0.3912 target = 0.133624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.109855 restraints weight = 18941.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.112903 restraints weight = 10746.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.114959 restraints weight = 7322.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.116171 restraints weight = 5652.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.117224 restraints weight = 4796.159| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8854 Z= 0.134 Angle : 0.581 7.751 11958 Z= 0.302 Chirality : 0.040 0.202 1375 Planarity : 0.004 0.060 1522 Dihedral : 5.792 50.963 1219 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 5.38 % Allowed : 26.45 % Favored : 68.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.25), residues: 1110 helix: 1.69 (0.19), residues: 715 sheet: -0.82 (0.63), residues: 68 loop : -0.83 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 559 TYR 0.019 0.001 TYR A 259 PHE 0.035 0.001 PHE A 974 TRP 0.016 0.001 TRP A 979 HIS 0.004 0.001 HIS A 375 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 8854) covalent geometry : angle 0.58147 (11958) hydrogen bonds : bond 0.04808 ( 597) hydrogen bonds : angle 4.67040 ( 1752) *********************** 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 191 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 141 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.8590 (tpt) cc_final: 0.8225 (mmm) REVERT: A 138 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8679 (tt) REVERT: A 162 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8268 (mp) REVERT: A 299 MET cc_start: 0.7868 (mmt) cc_final: 0.7520 (mmt) REVERT: A 311 MET cc_start: 0.7184 (tpp) cc_final: 0.6889 (tpp) REVERT: A 595 ILE cc_start: 0.9613 (OUTLIER) cc_final: 0.9380 (mm) REVERT: A 604 ILE cc_start: 0.8488 (OUTLIER) cc_final: 0.8111 (tt) REVERT: A 624 HIS cc_start: 0.8484 (OUTLIER) cc_final: 0.8021 (t-170) REVERT: A 741 MET cc_start: 0.7686 (tpp) cc_final: 0.7327 (tpp) REVERT: A 874 LEU cc_start: 0.7946 (mt) cc_final: 0.7605 (mt) REVERT: A 945 TYR cc_start: 0.7070 (t80) cc_final: 0.6543 (t80) REVERT: A 970 TYR cc_start: 0.8059 (OUTLIER) cc_final: 0.7386 (t80) REVERT: A 1032 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8088 (pm20) REVERT: A 1064 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7862 (ptp90) REVERT: A 1107 MET cc_start: 0.5752 (pmm) cc_final: 0.5511 (pmm) REVERT: A 1136 GLU cc_start: 0.7938 (tm-30) cc_final: 0.7565 (tm-30) outliers start: 50 outliers final: 29 residues processed: 181 average time/residue: 0.0794 time to fit residues: 21.3689 Evaluate side-chains 169 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 132 time to evaluate : 0.316 ------------------------------------------------------------------------------- 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 162 LEU Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 256 GLN 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 738 ILE Chi-restraints excluded: chain A residue 745 LEU 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 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 22 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 chunk 54 optimal weight: 9.9990 chunk 111 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 36 optimal weight: 0.0980 chunk 70 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 34 optimal weight: 7.9990 chunk 46 optimal weight: 5.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- 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 = 0.3873 r_free = 0.3873 target = 0.130784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.106817 restraints weight = 19069.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.109692 restraints weight = 10982.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.111764 restraints weight = 7599.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.113119 restraints weight = 5884.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.113883 restraints weight = 4962.394| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8854 Z= 0.192 Angle : 0.634 10.898 11958 Z= 0.330 Chirality : 0.043 0.257 1375 Planarity : 0.004 0.060 1522 Dihedral : 5.782 52.266 1217 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 5.91 % Allowed : 25.91 % Favored : 68.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.25), residues: 1110 helix: 1.65 (0.19), residues: 709 sheet: -1.07 (0.66), residues: 63 loop : -0.89 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 605 TYR 0.018 0.002 TYR A 259 PHE 0.054 0.002 PHE A 974 TRP 0.016 0.001 TRP A 979 HIS 0.005 0.001 HIS A 375 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 8854) covalent geometry : angle 0.63412 (11958) hydrogen bonds : bond 0.05104 ( 597) hydrogen bonds : angle 4.80288 ( 1752) *********************** 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: 55 poor density : 138 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.7328 (tmm) cc_final: 0.6988 (tmm) REVERT: A 138 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8612 (tp) REVERT: A 162 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8244 (mp) REVERT: A 299 MET cc_start: 0.7945 (mmt) cc_final: 0.7588 (mmt) REVERT: A 311 MET cc_start: 0.7241 (tpp) cc_final: 0.6870 (tpp) REVERT: A 315 PHE cc_start: 0.8678 (m-80) cc_final: 0.7940 (m-80) REVERT: A 347 PHE cc_start: 0.8261 (t80) cc_final: 0.7897 (t80) REVERT: A 595 ILE cc_start: 0.9573 (OUTLIER) cc_final: 0.9360 (mm) REVERT: A 604 ILE cc_start: 0.8479 (OUTLIER) cc_final: 0.8146 (tt) REVERT: A 624 HIS cc_start: 0.8524 (OUTLIER) cc_final: 0.8009 (t-170) REVERT: A 945 TYR cc_start: 0.7660 (t80) cc_final: 0.7221 (t80) REVERT: A 970 TYR cc_start: 0.8011 (OUTLIER) cc_final: 0.7385 (t80) REVERT: A 1032 GLU cc_start: 0.8828 (OUTLIER) cc_final: 0.8098 (pm20) REVERT: A 1064 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7890 (ptp90) REVERT: A 1136 GLU cc_start: 0.7993 (tm-30) cc_final: 0.7611 (tm-30) outliers start: 55 outliers final: 34 residues processed: 179 average time/residue: 0.0798 time to fit residues: 21.2346 Evaluate side-chains 175 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 133 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL 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 221 VAL 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 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 748 VAL 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 864 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 55 optimal weight: 5.9990 chunk 44 optimal weight: 0.6980 chunk 69 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 111 optimal weight: 7.9990 chunk 52 optimal weight: 0.4980 chunk 96 optimal weight: 0.8980 chunk 87 optimal weight: 0.0970 chunk 92 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 overall best weight: 1.2380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 GLN ** 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 = 0.3895 r_free = 0.3895 target = 0.132120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.108280 restraints weight = 18943.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.111317 restraints weight = 10909.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.113306 restraints weight = 7466.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.114672 restraints weight = 5794.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.115434 restraints weight = 4881.359| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8854 Z= 0.157 Angle : 0.638 14.109 11958 Z= 0.321 Chirality : 0.043 0.341 1375 Planarity : 0.004 0.059 1522 Dihedral : 5.669 53.618 1215 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 5.16 % Allowed : 27.96 % Favored : 66.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.25), residues: 1110 helix: 1.68 (0.19), residues: 715 sheet: -1.07 (0.66), residues: 63 loop : -0.89 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 605 TYR 0.019 0.001 TYR A 259 PHE 0.054 0.002 PHE A 974 TRP 0.015 0.001 TRP A 979 HIS 0.004 0.001 HIS A 375 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 8854) covalent geometry : angle 0.63760 (11958) hydrogen bonds : bond 0.05001 ( 597) hydrogen bonds : angle 4.73209 ( 1752) *********************** 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 187 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 139 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8559 (tp) REVERT: A 162 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8228 (mp) REVERT: A 216 PHE cc_start: 0.7433 (m-80) cc_final: 0.6950 (t80) REVERT: A 299 MET cc_start: 0.7845 (mmt) cc_final: 0.7441 (mmt) REVERT: A 311 MET cc_start: 0.7347 (tpp) cc_final: 0.6939 (tpp) REVERT: A 315 PHE cc_start: 0.8662 (m-80) cc_final: 0.7885 (m-80) REVERT: A 347 PHE cc_start: 0.8217 (t80) cc_final: 0.7852 (t80) REVERT: A 595 ILE cc_start: 0.9602 (OUTLIER) cc_final: 0.9372 (mm) REVERT: A 604 ILE cc_start: 0.8455 (OUTLIER) cc_final: 0.8094 (tt) REVERT: A 624 HIS cc_start: 0.8494 (OUTLIER) cc_final: 0.7981 (t-170) REVERT: A 945 TYR cc_start: 0.7589 (t80) cc_final: 0.7083 (t80) REVERT: A 970 TYR cc_start: 0.8036 (OUTLIER) cc_final: 0.7398 (t80) REVERT: A 1032 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8095 (pm20) REVERT: A 1064 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7718 (ptp90) REVERT: A 1136 GLU cc_start: 0.7953 (tm-30) cc_final: 0.7583 (tm-30) outliers start: 48 outliers final: 33 residues processed: 178 average time/residue: 0.0780 time to fit residues: 20.6390 Evaluate side-chains 175 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 134 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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 221 VAL 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 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 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 864 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 63 optimal weight: 0.9980 chunk 101 optimal weight: 0.3980 chunk 45 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 49 optimal weight: 9.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 = 0.3882 r_free = 0.3882 target = 0.131292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.107503 restraints weight = 18887.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.110489 restraints weight = 10920.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.112483 restraints weight = 7498.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.113818 restraints weight = 5830.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.114526 restraints weight = 4918.982| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8854 Z= 0.169 Angle : 0.638 14.429 11958 Z= 0.324 Chirality : 0.043 0.246 1375 Planarity : 0.004 0.061 1522 Dihedral : 5.727 54.950 1215 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 5.05 % Allowed : 28.92 % Favored : 66.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.25), residues: 1110 helix: 1.67 (0.19), residues: 716 sheet: -1.22 (0.65), residues: 63 loop : -0.93 (0.34), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 605 TYR 0.017 0.002 TYR A 259 PHE 0.045 0.002 PHE A 974 TRP 0.009 0.001 TRP A 327 HIS 0.004 0.001 HIS A 375 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 8854) covalent geometry : angle 0.63840 (11958) hydrogen bonds : bond 0.05016 ( 597) hydrogen bonds : angle 4.74633 ( 1752) *********************** 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 181 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 134 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8443 (tp) REVERT: A 162 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8247 (mp) REVERT: A 216 PHE cc_start: 0.7449 (m-80) cc_final: 0.6961 (t80) REVERT: A 299 MET cc_start: 0.7899 (mmt) cc_final: 0.7468 (mmt) REVERT: A 347 PHE cc_start: 0.8277 (t80) cc_final: 0.7878 (t80) REVERT: A 595 ILE cc_start: 0.9600 (OUTLIER) cc_final: 0.9370 (mm) REVERT: A 624 HIS cc_start: 0.8493 (OUTLIER) cc_final: 0.7699 (t-170) REVERT: A 874 LEU cc_start: 0.8534 (mt) cc_final: 0.8035 (tp) REVERT: A 945 TYR cc_start: 0.7628 (t80) cc_final: 0.7115 (t80) REVERT: A 970 TYR cc_start: 0.7938 (OUTLIER) cc_final: 0.7223 (t80) REVERT: A 1032 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8091 (pm20) REVERT: A 1064 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7879 (ptp90) REVERT: A 1136 GLU cc_start: 0.7978 (tm-30) cc_final: 0.7614 (tm-30) REVERT: A 1207 ILE cc_start: 0.8656 (mm) cc_final: 0.8108 (mt) outliers start: 47 outliers final: 33 residues processed: 171 average time/residue: 0.0798 time to fit residues: 20.2010 Evaluate side-chains 172 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 132 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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 162 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 290 HIS 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 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 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 864 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 8 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 100 optimal weight: 0.0970 chunk 75 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 4 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- 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 = 0.3854 r_free = 0.3854 target = 0.129409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.106352 restraints weight = 18832.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.108967 restraints weight = 11516.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.110709 restraints weight = 8224.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.111854 restraints weight = 6580.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.112629 restraints weight = 5661.857| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 8854 Z= 0.214 Angle : 0.689 14.645 11958 Z= 0.350 Chirality : 0.044 0.309 1375 Planarity : 0.005 0.062 1522 Dihedral : 5.861 56.351 1215 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.73 % Allowed : 29.25 % Favored : 66.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.25), residues: 1110 helix: 1.59 (0.19), residues: 710 sheet: -1.24 (0.69), residues: 58 loop : -0.97 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 479 TYR 0.017 0.002 TYR A 937 PHE 0.042 0.002 PHE A 974 TRP 0.010 0.001 TRP A 327 HIS 0.005 0.001 HIS A 375 Details of bonding type rmsd covalent geometry : bond 0.00461 ( 8854) covalent geometry : angle 0.68867 (11958) hydrogen bonds : bond 0.05279 ( 597) hydrogen bonds : angle 4.88095 ( 1752) *********************** 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 179 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 135 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: A 138 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8623 (tp) REVERT: A 162 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8423 (mp) REVERT: A 299 MET cc_start: 0.7915 (mmt) cc_final: 0.7540 (mmt) REVERT: A 311 MET cc_start: 0.7373 (tpp) cc_final: 0.7099 (tmm) REVERT: A 315 PHE cc_start: 0.8599 (m-80) cc_final: 0.8120 (m-80) REVERT: A 347 PHE cc_start: 0.8279 (t80) cc_final: 0.7878 (t80) REVERT: A 624 HIS cc_start: 0.8484 (OUTLIER) cc_final: 0.7571 (t-170) REVERT: A 741 MET cc_start: 0.7611 (tpp) cc_final: 0.7328 (tpp) REVERT: A 874 LEU cc_start: 0.8778 (mt) cc_final: 0.7974 (tp) REVERT: A 945 TYR cc_start: 0.7632 (t80) cc_final: 0.7156 (t80) REVERT: A 970 TYR cc_start: 0.7581 (OUTLIER) cc_final: 0.7247 (t80) REVERT: A 1136 GLU cc_start: 0.7927 (tm-30) cc_final: 0.7600 (tm-30) REVERT: A 1207 ILE cc_start: 0.8534 (mm) cc_final: 0.7987 (mt) outliers start: 44 outliers final: 35 residues processed: 168 average time/residue: 0.0808 time to fit residues: 19.8481 Evaluate side-chains 169 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 130 time to evaluate : 0.298 ------------------------------------------------------------------------------- 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 162 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 290 HIS Chi-restraints excluded: chain A residue 306 SER 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 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 748 VAL 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 864 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 1061 TYR Chi-restraints excluded: chain A residue 1077 VAL 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 23 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 1 optimal weight: 0.0050 chunk 95 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 chunk 88 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- 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** A1172 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.132210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.108599 restraints weight = 18581.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.111532 restraints weight = 10654.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.113588 restraints weight = 7354.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.114949 restraints weight = 5690.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.115660 restraints weight = 4785.256| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.1678 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 : 0.670 15.519 11958 Z= 0.330 Chirality : 0.043 0.309 1375 Planarity : 0.004 0.061 1522 Dihedral : 5.808 57.349 1215 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 4.41 % Allowed : 29.68 % Favored : 65.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.25), residues: 1110 helix: 1.72 (0.19), residues: 716 sheet: -0.96 (0.74), residues: 53 loop : -0.93 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 605 TYR 0.016 0.001 TYR A 259 PHE 0.019 0.001 PHE A1000 TRP 0.009 0.001 TRP A 327 HIS 0.003 0.001 HIS A 375 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 8854) covalent geometry : angle 0.66983 (11958) hydrogen bonds : bond 0.04901 ( 597) hydrogen bonds : angle 4.68396 ( 1752) *********************** 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 176 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 135 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: A 138 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8488 (tt) REVERT: A 162 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8208 (mp) REVERT: A 216 PHE cc_start: 0.7352 (m-80) cc_final: 0.6839 (t80) REVERT: A 299 MET cc_start: 0.7845 (mmt) cc_final: 0.7434 (mmt) REVERT: A 311 MET cc_start: 0.7479 (tpp) cc_final: 0.6915 (tpp) REVERT: A 315 PHE cc_start: 0.8702 (m-80) cc_final: 0.7920 (m-80) REVERT: A 347 PHE cc_start: 0.8246 (t80) cc_final: 0.7841 (t80) REVERT: A 488 GLU cc_start: 0.9015 (tm-30) cc_final: 0.8188 (tm-30) REVERT: A 624 HIS cc_start: 0.8458 (OUTLIER) cc_final: 0.7638 (t-170) REVERT: A 729 MET cc_start: 0.7463 (mmm) cc_final: 0.7157 (mmm) REVERT: A 741 MET cc_start: 0.7647 (tpp) cc_final: 0.7234 (tpp) REVERT: A 874 LEU cc_start: 0.8782 (mt) cc_final: 0.8067 (tp) REVERT: A 945 TYR cc_start: 0.7532 (t80) cc_final: 0.7051 (t80) REVERT: A 970 TYR cc_start: 0.7681 (OUTLIER) cc_final: 0.7330 (t80) REVERT: A 1136 GLU cc_start: 0.7955 (tm-30) cc_final: 0.7609 (tm-30) REVERT: A 1207 ILE cc_start: 0.8659 (mm) cc_final: 0.8115 (mt) outliers start: 41 outliers final: 32 residues processed: 168 average time/residue: 0.0790 time to fit residues: 19.8959 Evaluate side-chains 169 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 133 time to evaluate : 0.338 ------------------------------------------------------------------------------- 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 162 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 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 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 745 LEU 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 864 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 1061 TYR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 15 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 chunk 99 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3903 r_free = 0.3903 target = 0.132544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.108922 restraints weight = 18645.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.111927 restraints weight = 10700.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.113921 restraints weight = 7301.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.115232 restraints weight = 5666.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.115970 restraints weight = 4783.870| |-----------------------------------------------------------------------------| r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8854 Z= 0.142 Angle : 0.673 15.568 11958 Z= 0.331 Chirality : 0.042 0.247 1375 Planarity : 0.004 0.059 1522 Dihedral : 5.781 59.194 1215 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 4.19 % Allowed : 29.89 % Favored : 65.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.25), residues: 1110 helix: 1.78 (0.19), residues: 717 sheet: -1.00 (0.73), residues: 53 loop : -0.93 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 605 TYR 0.019 0.001 TYR A 322 PHE 0.018 0.001 PHE A1000 TRP 0.008 0.001 TRP A 327 HIS 0.004 0.001 HIS A 375 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 8854) covalent geometry : angle 0.67307 (11958) hydrogen bonds : bond 0.04771 ( 597) hydrogen bonds : angle 4.62726 ( 1752) ********************** 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 178 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 139 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: A 123 MET cc_start: 0.8628 (mmp) cc_final: 0.8400 (mmm) REVERT: A 138 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8640 (tt) REVERT: A 162 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8217 (mp) REVERT: A 216 PHE cc_start: 0.7317 (m-80) cc_final: 0.6817 (t80) REVERT: A 299 MET cc_start: 0.7891 (mmt) cc_final: 0.7464 (mmt) REVERT: A 347 PHE cc_start: 0.8047 (t80) cc_final: 0.7629 (t80) REVERT: A 488 GLU cc_start: 0.9015 (tm-30) cc_final: 0.8201 (tm-30) REVERT: A 624 HIS cc_start: 0.8401 (OUTLIER) cc_final: 0.7619 (t-170) REVERT: A 874 LEU cc_start: 0.8493 (mt) cc_final: 0.7818 (tp) REVERT: A 880 SER cc_start: 0.7528 (m) cc_final: 0.7205 (p) REVERT: A 945 TYR cc_start: 0.7549 (t80) cc_final: 0.7071 (t80) REVERT: A 970 TYR cc_start: 0.7639 (OUTLIER) cc_final: 0.7291 (t80) REVERT: A 1071 ARG cc_start: 0.6733 (mtm180) cc_final: 0.6390 (ptt-90) REVERT: A 1136 GLU cc_start: 0.7948 (tm-30) cc_final: 0.7605 (tm-30) REVERT: A 1207 ILE cc_start: 0.8653 (mm) cc_final: 0.8105 (mt) outliers start: 39 outliers final: 32 residues processed: 170 average time/residue: 0.0775 time to fit residues: 19.5252 Evaluate side-chains 171 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 135 time to evaluate : 0.358 ------------------------------------------------------------------------------- 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 162 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 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 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 745 LEU 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 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 1061 TYR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 103 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 4 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.3894 r_free = 0.3894 target = 0.131864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.108344 restraints weight = 18670.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.111231 restraints weight = 10725.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.113315 restraints weight = 7400.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.114698 restraints weight = 5707.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.115597 restraints weight = 4775.964| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8854 Z= 0.160 Angle : 0.687 16.041 11958 Z= 0.340 Chirality : 0.043 0.251 1375 Planarity : 0.004 0.059 1522 Dihedral : 5.801 59.711 1215 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.98 % Allowed : 30.22 % Favored : 65.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.25), residues: 1110 helix: 1.78 (0.19), residues: 717 sheet: -1.22 (0.68), residues: 58 loop : -0.95 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 605 TYR 0.014 0.001 TYR A 322 PHE 0.020 0.001 PHE A1000 TRP 0.008 0.001 TRP A 327 HIS 0.004 0.001 HIS A 375 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 8854) covalent geometry : angle 0.68720 (11958) hydrogen bonds : bond 0.04822 ( 597) hydrogen bonds : angle 4.65957 ( 1752) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1456.03 seconds wall clock time: 26 minutes 4.18 seconds (1564.18 seconds total)