Starting phenix.real_space_refine on Sun Aug 24 11:09:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sx8_40827/08_2025/8sx8_40827_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sx8_40827/08_2025/8sx8_40827.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sx8_40827/08_2025/8sx8_40827.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sx8_40827/08_2025/8sx8_40827.map" model { file = "/net/cci-nas-00/data/ceres_data/8sx8_40827/08_2025/8sx8_40827_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sx8_40827/08_2025/8sx8_40827_trim.cif" } resolution = 3.5 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= 0.001 sd= 0.049 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: 5 Type Number sf(0) Gaussians S 36 5.16 5 C 6117 2.51 5 N 1580 2.21 5 O 1682 1.98 5 H 9610 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 62 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19025 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 18997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1175, 18997 Classifications: {'peptide': 1175} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 1139} Chain breaks: 3 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'XPG': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 4.02, per 1000 atoms: 0.21 Number of scatterers: 19025 At special positions: 0 Unit cell: (82.665, 96.86, 145.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 36 16.00 O 1682 8.00 N 1580 7.00 C 6117 6.00 H 9610 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.09 Conformation dependent library (CDL) restraints added in 650.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2220 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 6 sheets defined 72.3% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 24 through 26 No H-bonds generated for 'chain 'A' and resid 24 through 26' Processing helix chain 'A' and resid 27 through 37 Processing helix chain 'A' and resid 40 through 44 removed outlier: 4.036A pdb=" N MET A 44 " --> pdb=" O GLU A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 51 Processing helix chain 'A' and resid 52 through 74 removed outlier: 3.689A pdb=" N GLU A 58 " --> pdb=" O GLN A 54 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LEU A 60 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TYR A 63 " --> pdb=" O GLU A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 93 removed outlier: 6.434A pdb=" N LYS A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N SER A 91 " --> pdb=" O CYS A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 122 removed outlier: 3.530A pdb=" N THR A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Proline residue: A 110 - end of helix removed outlier: 3.513A pdb=" N PHE A 120 " --> pdb=" O ILE A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 180 removed outlier: 4.067A pdb=" N ARG A 180 " --> pdb=" O ARG A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 188 Processing helix chain 'A' and resid 190 through 201 removed outlier: 3.766A pdb=" N LEU A 198 " --> pdb=" O ILE A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 208 removed outlier: 3.941A pdb=" N ASP A 206 " --> pdb=" O ASN A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 234 Proline residue: A 219 - end of helix Processing helix chain 'A' and resid 236 through 289 removed outlier: 3.950A pdb=" N GLY A 240 " --> pdb=" O SER A 236 " (cutoff:3.500A) Proline residue: A 249 - end of helix removed outlier: 4.130A pdb=" N ALA A 267 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N ARG A 284 " --> pdb=" O ILE A 280 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE A 285 " --> pdb=" O THR A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 342 removed outlier: 3.567A pdb=" N PHE A 295 " --> pdb=" O TRP A 291 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG A 312 " --> pdb=" O SER A 308 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N SER A 328 " --> pdb=" O PHE A 324 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N LYS A 329 " --> pdb=" O PHE A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 367 removed outlier: 3.708A pdb=" N ALA A 360 " --> pdb=" O SER A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 391 removed outlier: 3.553A pdb=" N VAL A 381 " --> pdb=" O SER A 377 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER A 382 " --> pdb=" O GLU A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 459 Processing helix chain 'A' and resid 489 through 495 Processing helix chain 'A' and resid 500 through 511 Processing helix chain 'A' and resid 513 through 520 Processing helix chain 'A' and resid 522 through 525 Processing helix chain 'A' and resid 536 through 551 Processing helix chain 'A' and resid 561 through 565 removed outlier: 4.306A pdb=" N ALA A 564 " --> pdb=" O PRO A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 577 Processing helix chain 'A' and resid 581 through 585 removed outlier: 4.436A pdb=" N GLU A 584 " --> pdb=" O ALA A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 598 removed outlier: 3.815A pdb=" N LEU A 597 " --> pdb=" O GLN A 593 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LYS A 598 " --> pdb=" O LEU A 594 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 593 through 598' Processing helix chain 'A' and resid 697 through 707 removed outlier: 3.816A pdb=" N TYR A 701 " --> pdb=" O GLY A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 745 removed outlier: 3.660A pdb=" N ILE A 714 " --> pdb=" O HIS A 710 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASP A 732 " --> pdb=" O TYR A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 808 removed outlier: 3.743A pdb=" N GLY A 766 " --> pdb=" O ASN A 762 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE A 787 " --> pdb=" O SER A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 815 removed outlier: 3.851A pdb=" N PHE A 813 " --> pdb=" O PRO A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 827 removed outlier: 3.523A pdb=" N ILE A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ARG A 824 " --> pdb=" O ARG A 820 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE A 825 " --> pdb=" O ILE A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 834 Processing helix chain 'A' and resid 834 through 861 removed outlier: 4.223A pdb=" N LEU A 838 " --> pdb=" O ASP A 834 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN A 849 " --> pdb=" O GLN A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 910 Proline residue: A 870 - end of helix removed outlier: 4.074A pdb=" N THR A 885 " --> pdb=" O TYR A 881 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ASP A 888 " --> pdb=" O GLU A 884 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER A 898 " --> pdb=" O SER A 894 " (cutoff:3.500A) Proline residue: A 899 - end of helix Processing helix chain 'A' and resid 910 through 917 Processing helix chain 'A' and resid 919 through 970 removed outlier: 3.606A pdb=" N ARG A 951 " --> pdb=" O TRP A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 987 Processing helix chain 'A' and resid 988 through 1017 removed outlier: 3.778A pdb=" N MET A 992 " --> pdb=" O THR A 988 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLN A 994 " --> pdb=" O MET A 990 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG A 998 " --> pdb=" O GLN A 994 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU A1002 " --> pdb=" O ARG A 998 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE A1008 " --> pdb=" O GLU A1004 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N SER A1009 " --> pdb=" O ASN A1005 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N TYR A1016 " --> pdb=" O ARG A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1080 through 1089 removed outlier: 3.744A pdb=" N ILE A1085 " --> pdb=" O LYS A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1106 through 1108 No H-bonds generated for 'chain 'A' and resid 1106 through 1108' Processing helix chain 'A' and resid 1109 through 1114 Processing helix chain 'A' and resid 1130 through 1136 Processing helix chain 'A' and resid 1144 through 1153 Processing helix chain 'A' and resid 1155 through 1160 Processing helix chain 'A' and resid 1171 through 1175 Processing helix chain 'A' and resid 1178 through 1193 Processing helix chain 'A' and resid 1210 through 1223 Processing helix chain 'A' and resid 1224 through 1226 No H-bonds generated for 'chain 'A' and resid 1224 through 1226' Processing helix chain 'A' and resid 1234 through 1239 removed outlier: 3.525A pdb=" N ILE A1239 " --> pdb=" O ASN A1236 " (cutoff:3.500A) Processing helix chain 'A' and resid 1257 through 1264 Processing helix chain 'A' and resid 1267 through 1274 Processing helix chain 'A' and resid 1277 through 1297 Processing sheet with id=AA1, first strand: chain 'A' and resid 428 through 435 removed outlier: 5.733A pdb=" N GLN A 429 " --> pdb=" O ALA A 417 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ALA A 417 " --> pdb=" O GLN A 429 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N PHE A 433 " --> pdb=" O GLN A 413 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N GLN A 413 " --> pdb=" O PHE A 433 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N VAL A 435 " --> pdb=" O ASN A 411 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N ASN A 411 " --> pdb=" O VAL A 435 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N PHE A 415 " --> pdb=" O GLN A 466 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N GLN A 466 " --> pdb=" O PHE A 415 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 475 through 478 removed outlier: 6.361A pdb=" N ALA A 476 " --> pdb=" O LEU A 557 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ASP A 559 " --> pdb=" O ALA A 476 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL A 478 " --> pdb=" O ASP A 559 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU A 441 " --> pdb=" O LEU A 589 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LEU A 440 " --> pdb=" O GLN A 602 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N LEU A 604 " --> pdb=" O LEU A 440 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ALA A 442 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N LEU A 606 " --> pdb=" O ALA A 442 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL A 444 " --> pdb=" O LEU A 606 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LYS A 607 " --> pdb=" O MET A 611 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N MET A 611 " --> pdb=" O LYS A 607 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 487 through 488 removed outlier: 3.787A pdb=" N GLY A 487 " --> pdb=" O ILE A 528 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1058 through 1065 removed outlier: 6.400A pdb=" N LYS A1059 " --> pdb=" O ASN A1047 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ASN A1047 " --> pdb=" O LYS A1059 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N LEU A1061 " --> pdb=" O ASN A1045 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N VAL A1046 " --> pdb=" O GLU A1095 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLU A1095 " --> pdb=" O VAL A1046 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1071 through 1075 removed outlier: 6.428A pdb=" N GLY A1072 " --> pdb=" O MET A1245 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N LEU A1247 " --> pdb=" O GLY A1072 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL A1074 " --> pdb=" O LEU A1247 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ASP A1248 " --> pdb=" O LEU A1252 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N LEU A1252 " --> pdb=" O ASP A1248 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1118 through 1120 removed outlier: 6.206A pdb=" N SER A1118 " --> pdb=" O ILE A1199 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LEU A1198 " --> pdb=" O LEU A1229 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 615 hydrogen bonds defined for protein. 1797 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.93 Time building geometry restraints manager: 2.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9593 1.03 - 1.23: 24 1.23 - 1.42: 3988 1.42 - 1.61: 5562 1.61 - 1.81: 59 Bond restraints: 19226 Sorted by residual: bond pdb=" CB GLU A1202 " pdb=" HB2 GLU A1202 " ideal model delta sigma weight residual 0.970 1.091 -0.121 2.00e-02 2.50e+03 3.66e+01 bond pdb=" CG GLU A1202 " pdb=" HG3 GLU A1202 " ideal model delta sigma weight residual 0.970 1.090 -0.120 2.00e-02 2.50e+03 3.59e+01 bond pdb=" CG GLU A1202 " pdb=" HG2 GLU A1202 " ideal model delta sigma weight residual 0.970 1.090 -0.120 2.00e-02 2.50e+03 3.57e+01 bond pdb=" CB GLU A1202 " pdb=" HB3 GLU A1202 " ideal model delta sigma weight residual 0.970 1.089 -0.119 2.00e-02 2.50e+03 3.57e+01 bond pdb=" C1 XPG A1401 " pdb=" O1A XPG A1401 " ideal model delta sigma weight residual 1.250 1.217 0.033 2.00e-02 2.50e+03 2.71e+00 ... (remaining 19221 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 31991 1.36 - 2.73: 2614 2.73 - 4.09: 165 4.09 - 5.46: 25 5.46 - 6.82: 7 Bond angle restraints: 34802 Sorted by residual: angle pdb=" CA ARG A 951 " pdb=" CB ARG A 951 " pdb=" CG ARG A 951 " ideal model delta sigma weight residual 114.10 107.28 6.82 2.00e+00 2.50e-01 1.16e+01 angle pdb=" C LEU A 181 " pdb=" N SER A 182 " pdb=" CA SER A 182 " ideal model delta sigma weight residual 120.71 125.30 -4.59 1.42e+00 4.96e-01 1.04e+01 angle pdb=" CA TYR A 985 " pdb=" CB TYR A 985 " pdb=" CG TYR A 985 " ideal model delta sigma weight residual 113.90 108.18 5.72 1.80e+00 3.09e-01 1.01e+01 angle pdb=" CA HIS A 153 " pdb=" CB HIS A 153 " pdb=" CG HIS A 153 " ideal model delta sigma weight residual 113.80 110.70 3.10 1.00e+00 1.00e+00 9.58e+00 angle pdb=" CA PHE A 336 " pdb=" CB PHE A 336 " pdb=" CG PHE A 336 " ideal model delta sigma weight residual 113.80 110.80 3.00 1.00e+00 1.00e+00 9.00e+00 ... (remaining 34797 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.03: 8187 17.03 - 34.05: 457 34.05 - 51.08: 147 51.08 - 68.10: 160 68.10 - 85.13: 20 Dihedral angle restraints: 8971 sinusoidal: 4863 harmonic: 4108 Sorted by residual: dihedral pdb=" CA PRO A1094 " pdb=" C PRO A1094 " pdb=" N GLU A1095 " pdb=" CA GLU A1095 " ideal model delta harmonic sigma weight residual 180.00 152.51 27.49 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CA GLY A 282 " pdb=" C GLY A 282 " pdb=" N ILE A 283 " pdb=" CA ILE A 283 " ideal model delta harmonic sigma weight residual -180.00 -152.58 -27.42 0 5.00e+00 4.00e-02 3.01e+01 dihedral pdb=" CA ARG A1114 " pdb=" C ARG A1114 " pdb=" N LYS A1115 " pdb=" CA LYS A1115 " ideal model delta harmonic sigma weight residual 180.00 156.07 23.93 0 5.00e+00 4.00e-02 2.29e+01 ... (remaining 8968 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1013 0.049 - 0.099: 376 0.099 - 0.148: 91 0.148 - 0.197: 19 0.197 - 0.247: 7 Chirality restraints: 1506 Sorted by residual: chirality pdb=" CA HIS A 153 " pdb=" N HIS A 153 " pdb=" C HIS A 153 " pdb=" CB HIS A 153 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" C8 XPG A1401 " pdb=" C12 XPG A1401 " pdb=" C7 XPG A1401 " pdb=" C9 XPG A1401 " both_signs ideal model delta sigma weight residual False -2.54 -2.78 0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA THR A 366 " pdb=" N THR A 366 " pdb=" C THR A 366 " pdb=" CB THR A 366 " both_signs ideal model delta sigma weight residual False 2.53 2.31 0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 1503 not shown) Planarity restraints: 2757 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 216 " 0.035 2.00e-02 2.50e+03 3.43e-02 4.70e+01 pdb=" CG TRP A 216 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TRP A 216 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP A 216 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 216 " -0.096 2.00e-02 2.50e+03 pdb=" CE2 TRP A 216 " -0.013 2.00e-02 2.50e+03 pdb=" CE3 TRP A 216 " 0.013 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 216 " -0.011 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 216 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 216 " -0.002 2.00e-02 2.50e+03 pdb=" HD1 TRP A 216 " -0.001 2.00e-02 2.50e+03 pdb=" HE1 TRP A 216 " 0.086 2.00e-02 2.50e+03 pdb=" HE3 TRP A 216 " -0.005 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 216 " 0.015 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 216 " 0.001 2.00e-02 2.50e+03 pdb=" HH2 TRP A 216 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 994 " 0.042 2.00e-02 2.50e+03 5.12e-02 3.93e+01 pdb=" CD GLN A 994 " -0.038 2.00e-02 2.50e+03 pdb=" OE1 GLN A 994 " -0.000 2.00e-02 2.50e+03 pdb=" NE2 GLN A 994 " -0.080 2.00e-02 2.50e+03 pdb="HE21 GLN A 994 " -0.003 2.00e-02 2.50e+03 pdb="HE22 GLN A 994 " 0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 362 " -0.348 9.50e-02 1.11e+02 1.20e-01 3.71e+01 pdb=" NE ARG A 362 " -0.002 2.00e-02 2.50e+03 pdb=" CZ ARG A 362 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 362 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG A 362 " 0.064 2.00e-02 2.50e+03 pdb="HH11 ARG A 362 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG A 362 " 0.021 2.00e-02 2.50e+03 pdb="HH21 ARG A 362 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 362 " -0.068 2.00e-02 2.50e+03 ... (remaining 2754 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.16: 722 2.16 - 2.77: 36465 2.77 - 3.38: 54063 3.38 - 3.99: 66173 3.99 - 4.60: 106360 Nonbonded interactions: 263783 Sorted by model distance: nonbonded pdb=" OD1 ASN A 544 " pdb="HH12 ARG A 547 " model vdw 1.545 2.450 nonbonded pdb=" HG SER A1051 " pdb=" OD1 ASP A1053 " model vdw 1.569 2.450 nonbonded pdb=" HG SER A1049 " pdb=" O PRO A1055 " model vdw 1.598 2.450 nonbonded pdb=" OE1 GLU A1020 " pdb=" H GLU A1020 " model vdw 1.598 2.450 nonbonded pdb=" HG1 THR A 269 " pdb=" OE2 GLU A 306 " model vdw 1.602 2.450 ... (remaining 263778 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=0.00 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: 2.700 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: 0.130 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 21.760 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 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 : 0.005 0.039 9616 Z= 0.232 Angle : 0.839 6.820 13029 Z= 0.507 Chirality : 0.056 0.247 1506 Planarity : 0.009 0.136 1621 Dihedral : 12.224 85.125 3524 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 0.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.10 % Allowed : 1.18 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.93 (0.21), residues: 1167 helix: -1.46 (0.15), residues: 767 sheet: -0.48 (0.49), residues: 73 loop : -0.40 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.003 ARG A 350 TYR 0.038 0.006 TYR A 155 PHE 0.031 0.004 PHE A 948 TRP 0.048 0.006 TRP A 216 HIS 0.025 0.004 HIS A 153 Details of bonding type rmsd covalent geometry : bond 0.00489 ( 9616) covalent geometry : angle 0.83855 (13029) hydrogen bonds : bond 0.19154 ( 615) hydrogen bonds : angle 7.94408 ( 1797) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 171 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ILE cc_start: 0.8362 (mm) cc_final: 0.8108 (mt) REVERT: A 276 MET cc_start: 0.7745 (mmm) cc_final: 0.7464 (mmt) REVERT: A 768 TYR cc_start: 0.7837 (t80) cc_final: 0.7489 (t80) REVERT: A 892 LEU cc_start: 0.8513 (tp) cc_final: 0.8293 (tp) REVERT: A 1007 MET cc_start: 0.8796 (mmm) cc_final: 0.7990 (mmm) REVERT: A 1083 SER cc_start: 0.8924 (m) cc_final: 0.8720 (p) REVERT: A 1256 ASP cc_start: 0.8679 (t0) cc_final: 0.8319 (t70) outliers start: 1 outliers final: 0 residues processed: 172 average time/residue: 0.3070 time to fit residues: 68.6718 Evaluate side-chains 114 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 30.0000 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 20.0000 chunk 100 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 741 GLN A 845 GLN A 999 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.174198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.125356 restraints weight = 45755.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.125419 restraints weight = 19770.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.126688 restraints weight = 13962.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.127657 restraints weight = 12157.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.127624 restraints weight = 11134.541| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9616 Z= 0.191 Angle : 0.628 6.297 13029 Z= 0.348 Chirality : 0.040 0.153 1506 Planarity : 0.005 0.047 1621 Dihedral : 5.320 39.573 1304 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 0.78 % Allowed : 6.07 % Favored : 93.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.16 (0.23), residues: 1167 helix: 0.31 (0.18), residues: 759 sheet: -1.18 (0.48), residues: 73 loop : 0.35 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1193 TYR 0.013 0.002 TYR A 137 PHE 0.022 0.002 PHE A 324 TRP 0.011 0.001 TRP A 733 HIS 0.008 0.002 HIS A 55 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 9616) covalent geometry : angle 0.62792 (13029) hydrogen bonds : bond 0.06702 ( 615) hydrogen bonds : angle 5.30975 ( 1797) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 122 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1146 LEU cc_start: 0.7777 (mt) cc_final: 0.7566 (mt) REVERT: A 1256 ASP cc_start: 0.8778 (t0) cc_final: 0.8373 (t70) outliers start: 8 outliers final: 8 residues processed: 127 average time/residue: 0.2917 time to fit residues: 49.7601 Evaluate side-chains 114 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 106 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 826 SER Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1119 ILE Chi-restraints excluded: chain A residue 1208 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 38 optimal weight: 20.0000 chunk 33 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 102 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 13 optimal weight: 0.4980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.174795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.125651 restraints weight = 45870.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.126137 restraints weight = 20478.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.127376 restraints weight = 13840.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.128243 restraints weight = 12156.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.128404 restraints weight = 10736.889| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9616 Z= 0.173 Angle : 0.555 5.402 13029 Z= 0.306 Chirality : 0.038 0.141 1506 Planarity : 0.004 0.045 1621 Dihedral : 5.086 37.212 1304 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.08 % Allowed : 7.25 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.79 (0.24), residues: 1167 helix: 0.86 (0.18), residues: 759 sheet: -1.60 (0.46), residues: 75 loop : 0.59 (0.36), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A1114 TYR 0.009 0.001 TYR A 728 PHE 0.021 0.002 PHE A 324 TRP 0.009 0.001 TRP A 733 HIS 0.007 0.001 HIS A 153 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 9616) covalent geometry : angle 0.55479 (13029) hydrogen bonds : bond 0.06093 ( 615) hydrogen bonds : angle 4.94053 ( 1797) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 MET cc_start: 0.7632 (mmm) cc_final: 0.7284 (mmt) REVERT: A 1256 ASP cc_start: 0.8724 (t0) cc_final: 0.8258 (t70) outliers start: 11 outliers final: 9 residues processed: 123 average time/residue: 0.2657 time to fit residues: 44.7893 Evaluate side-chains 111 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 102 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 826 SER Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1092 SER Chi-restraints excluded: chain A residue 1119 ILE Chi-restraints excluded: chain A residue 1197 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 1 optimal weight: 9.9990 chunk 22 optimal weight: 0.0370 chunk 97 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.8660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.177472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.129609 restraints weight = 45874.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.129792 restraints weight = 20066.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.131524 restraints weight = 13319.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.132077 restraints weight = 11492.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.132159 restraints weight = 10559.812| |-----------------------------------------------------------------------------| r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9616 Z= 0.127 Angle : 0.514 5.240 13029 Z= 0.279 Chirality : 0.037 0.153 1506 Planarity : 0.004 0.044 1621 Dihedral : 4.865 35.964 1304 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.08 % Allowed : 8.52 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.30 (0.25), residues: 1167 helix: 1.31 (0.19), residues: 755 sheet: -1.71 (0.46), residues: 74 loop : 0.75 (0.37), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 503 TYR 0.012 0.001 TYR A 92 PHE 0.017 0.001 PHE A 336 TRP 0.009 0.001 TRP A 733 HIS 0.004 0.001 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 9616) covalent geometry : angle 0.51439 (13029) hydrogen bonds : bond 0.05425 ( 615) hydrogen bonds : angle 4.62135 ( 1797) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1220 ARG cc_start: 0.8720 (mtm-85) cc_final: 0.8324 (mmm-85) REVERT: A 1256 ASP cc_start: 0.8706 (t0) cc_final: 0.8338 (t70) outliers start: 11 outliers final: 8 residues processed: 116 average time/residue: 0.2569 time to fit residues: 41.6044 Evaluate side-chains 110 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 826 SER Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1092 SER Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1197 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 38 optimal weight: 20.0000 chunk 91 optimal weight: 0.7980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.176838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.127782 restraints weight = 45778.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.127442 restraints weight = 22346.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.129702 restraints weight = 13924.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.130123 restraints weight = 11477.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.130260 restraints weight = 10874.658| |-----------------------------------------------------------------------------| r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9616 Z= 0.160 Angle : 0.523 4.933 13029 Z= 0.286 Chirality : 0.037 0.136 1506 Planarity : 0.004 0.045 1621 Dihedral : 4.762 36.493 1304 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.18 % Allowed : 8.72 % Favored : 90.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.37 (0.25), residues: 1167 helix: 1.37 (0.19), residues: 755 sheet: -1.61 (0.47), residues: 74 loop : 0.73 (0.37), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 503 TYR 0.008 0.001 TYR A1016 PHE 0.019 0.001 PHE A 336 TRP 0.009 0.001 TRP A 733 HIS 0.007 0.001 HIS A 153 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 9616) covalent geometry : angle 0.52259 (13029) hydrogen bonds : bond 0.05345 ( 615) hydrogen bonds : angle 4.59592 ( 1797) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1256 ASP cc_start: 0.8734 (t0) cc_final: 0.8374 (t70) outliers start: 12 outliers final: 10 residues processed: 115 average time/residue: 0.2608 time to fit residues: 41.4251 Evaluate side-chains 112 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 826 SER Chi-restraints excluded: chain A residue 1047 ASN Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1092 SER Chi-restraints excluded: chain A residue 1119 ILE Chi-restraints excluded: chain A residue 1208 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 86 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 94 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.176511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.128235 restraints weight = 45727.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.128125 restraints weight = 20882.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.129864 restraints weight = 13456.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.130533 restraints weight = 11205.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.130632 restraints weight = 10323.342| |-----------------------------------------------------------------------------| r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9616 Z= 0.160 Angle : 0.510 4.861 13029 Z= 0.279 Chirality : 0.037 0.153 1506 Planarity : 0.004 0.045 1621 Dihedral : 4.693 37.399 1304 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.27 % Allowed : 7.93 % Favored : 90.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.49 (0.25), residues: 1167 helix: 1.47 (0.19), residues: 755 sheet: -1.64 (0.47), residues: 75 loop : 0.77 (0.37), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 503 TYR 0.009 0.001 TYR A1255 PHE 0.019 0.001 PHE A 336 TRP 0.009 0.001 TRP A 733 HIS 0.006 0.001 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 9616) covalent geometry : angle 0.50953 (13029) hydrogen bonds : bond 0.05211 ( 615) hydrogen bonds : angle 4.48364 ( 1797) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1220 ARG cc_start: 0.8660 (mtm-85) cc_final: 0.8145 (mmm-85) REVERT: A 1256 ASP cc_start: 0.8758 (t0) cc_final: 0.8399 (t70) outliers start: 13 outliers final: 11 residues processed: 118 average time/residue: 0.2562 time to fit residues: 42.3587 Evaluate side-chains 111 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 826 SER Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 1047 ASN Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1092 SER Chi-restraints excluded: chain A residue 1197 ILE Chi-restraints excluded: chain A residue 1208 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 41 optimal weight: 20.0000 chunk 80 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 8 optimal weight: 0.5980 chunk 74 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 105 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.174836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.125652 restraints weight = 45492.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.125822 restraints weight = 20848.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.127482 restraints weight = 14499.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.128563 restraints weight = 11642.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.128383 restraints weight = 10759.928| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9616 Z= 0.134 Angle : 0.494 4.792 13029 Z= 0.269 Chirality : 0.037 0.158 1506 Planarity : 0.004 0.044 1621 Dihedral : 4.613 37.046 1304 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.18 % Allowed : 8.42 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.62 (0.25), residues: 1167 helix: 1.60 (0.19), residues: 756 sheet: -1.72 (0.48), residues: 75 loop : 0.80 (0.37), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 547 TYR 0.007 0.001 TYR A1016 PHE 0.017 0.001 PHE A 336 TRP 0.009 0.001 TRP A 733 HIS 0.005 0.001 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 9616) covalent geometry : angle 0.49386 (13029) hydrogen bonds : bond 0.05056 ( 615) hydrogen bonds : angle 4.37251 ( 1797) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1256 ASP cc_start: 0.8863 (t0) cc_final: 0.8468 (t70) outliers start: 12 outliers final: 11 residues processed: 116 average time/residue: 0.2607 time to fit residues: 42.3181 Evaluate side-chains 114 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 826 SER Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain A residue 1047 ASN Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1092 SER Chi-restraints excluded: chain A residue 1208 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 40 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 49 optimal weight: 20.0000 chunk 102 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 51 optimal weight: 20.0000 chunk 24 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.174947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.125863 restraints weight = 45716.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.126290 restraints weight = 20740.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.128306 restraints weight = 14238.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.128956 restraints weight = 11639.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.128939 restraints weight = 10699.322| |-----------------------------------------------------------------------------| r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9616 Z= 0.135 Angle : 0.503 6.965 13029 Z= 0.271 Chirality : 0.037 0.150 1506 Planarity : 0.004 0.043 1621 Dihedral : 4.568 40.495 1304 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.08 % Allowed : 8.62 % Favored : 90.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.72 (0.25), residues: 1167 helix: 1.70 (0.19), residues: 756 sheet: -1.80 (0.48), residues: 75 loop : 0.80 (0.37), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 503 TYR 0.009 0.001 TYR A1255 PHE 0.018 0.001 PHE A 336 TRP 0.009 0.001 TRP A 733 HIS 0.005 0.001 HIS A 798 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 9616) covalent geometry : angle 0.50281 (13029) hydrogen bonds : bond 0.04897 ( 615) hydrogen bonds : angle 4.29032 ( 1797) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1256 ASP cc_start: 0.8840 (t0) cc_final: 0.8369 (t70) outliers start: 11 outliers final: 10 residues processed: 113 average time/residue: 0.2527 time to fit residues: 40.2856 Evaluate side-chains 111 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 826 SER Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain A residue 1047 ASN Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1092 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 94 optimal weight: 9.9990 chunk 31 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 32 optimal weight: 0.5980 chunk 55 optimal weight: 10.0000 chunk 93 optimal weight: 0.3980 chunk 45 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 56 optimal weight: 20.0000 chunk 100 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.177453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.129484 restraints weight = 45497.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.129810 restraints weight = 20348.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.131584 restraints weight = 13937.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.132196 restraints weight = 11343.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.132292 restraints weight = 10288.538| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.4087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9616 Z= 0.117 Angle : 0.487 9.290 13029 Z= 0.261 Chirality : 0.036 0.144 1506 Planarity : 0.003 0.043 1621 Dihedral : 4.513 41.061 1304 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.78 % Allowed : 9.01 % Favored : 90.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.84 (0.25), residues: 1167 helix: 1.82 (0.19), residues: 755 sheet: -1.92 (0.48), residues: 75 loop : 0.81 (0.38), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 503 TYR 0.011 0.001 TYR A1255 PHE 0.025 0.001 PHE A 882 TRP 0.008 0.001 TRP A 733 HIS 0.004 0.001 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 9616) covalent geometry : angle 0.48668 (13029) hydrogen bonds : bond 0.04762 ( 615) hydrogen bonds : angle 4.18849 ( 1797) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 8 residues processed: 115 average time/residue: 0.2483 time to fit residues: 39.8626 Evaluate side-chains 113 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 105 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 1047 ASN Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1092 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 111 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 53 optimal weight: 20.0000 chunk 87 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 78 optimal weight: 8.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.175750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.122835 restraints weight = 45912.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.127414 restraints weight = 19211.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.130194 restraints weight = 12205.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.131235 restraints weight = 9708.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.132178 restraints weight = 8824.338| |-----------------------------------------------------------------------------| r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.4130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9616 Z= 0.174 Angle : 0.520 6.966 13029 Z= 0.284 Chirality : 0.038 0.138 1506 Planarity : 0.004 0.043 1621 Dihedral : 4.553 40.395 1304 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.88 % Allowed : 9.01 % Favored : 90.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.63 (0.25), residues: 1167 helix: 1.63 (0.19), residues: 756 sheet: -1.88 (0.49), residues: 74 loop : 0.77 (0.37), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 887 TYR 0.010 0.001 TYR A1255 PHE 0.030 0.002 PHE A 948 TRP 0.009 0.001 TRP A 733 HIS 0.007 0.001 HIS A 798 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 9616) covalent geometry : angle 0.51984 (13029) hydrogen bonds : bond 0.04979 ( 615) hydrogen bonds : angle 4.34241 ( 1797) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 8 residues processed: 111 average time/residue: 0.2359 time to fit residues: 36.6414 Evaluate side-chains 112 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 104 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1092 SER Chi-restraints excluded: chain A residue 1208 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 81 optimal weight: 3.9990 chunk 56 optimal weight: 0.4980 chunk 50 optimal weight: 7.9990 chunk 74 optimal weight: 0.9980 chunk 116 optimal weight: 9.9990 chunk 57 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 55 optimal weight: 20.0000 chunk 97 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.177316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.129726 restraints weight = 46055.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.129631 restraints weight = 20698.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.131444 restraints weight = 13933.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.132111 restraints weight = 11779.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.132075 restraints weight = 11074.963| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.4204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9616 Z= 0.121 Angle : 0.489 6.577 13029 Z= 0.264 Chirality : 0.036 0.136 1506 Planarity : 0.003 0.043 1621 Dihedral : 4.495 41.217 1304 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.88 % Allowed : 9.01 % Favored : 90.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.84 (0.25), residues: 1167 helix: 1.81 (0.19), residues: 756 sheet: -1.85 (0.49), residues: 74 loop : 0.81 (0.37), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 503 TYR 0.008 0.001 TYR A1016 PHE 0.030 0.001 PHE A 882 TRP 0.009 0.001 TRP A 733 HIS 0.005 0.001 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 9616) covalent geometry : angle 0.48867 (13029) hydrogen bonds : bond 0.04770 ( 615) hydrogen bonds : angle 4.18286 ( 1797) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3292.07 seconds wall clock time: 56 minutes 54.78 seconds (3414.78 seconds total)