Starting phenix.real_space_refine on Tue Nov 19 12:02:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sx8_40827/11_2024/8sx8_40827_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sx8_40827/11_2024/8sx8_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sx8_40827/11_2024/8sx8_40827.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sx8_40827/11_2024/8sx8_40827.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sx8_40827/11_2024/8sx8_40827_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sx8_40827/11_2024/8sx8_40827_trim.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/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: 9.38, per 1000 atoms: 0.49 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: 5.54 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.65 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: 7.99 Time building geometry restraints manager: 6.44 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: 1.440 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: 0.330 Extract box with map and model: 0.850 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 43.560 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.620 ------------------------------------------------------------------------------- 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= 0.319 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (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 TRP 0.048 0.006 TRP A 216 HIS 0.025 0.004 HIS A 153 PHE 0.031 0.004 PHE A 948 TYR 0.038 0.006 TYR A 155 ARG 0.014 0.003 ARG A 350 *********************** 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 : 1.569 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 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: 0.7488 (t80) REVERT: A 892 LEU cc_start: 0.8513 (tp) cc_final: 0.8278 (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: 0.8719 (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: 0.6222 time to fit residues: 141.1729 Evaluate side-chains 115 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 49 optimal weight: 30.0000 chunk 30 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 47 optimal weight: 9.9990 chunk 91 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 55 optimal weight: 30.0000 chunk 68 optimal weight: 0.0470 chunk 106 optimal weight: 4.9990 overall best weight: 1.7884 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9616 Z= 0.262 Angle : 0.625 6.299 13029 Z= 0.349 Chirality : 0.040 0.154 1506 Planarity : 0.005 0.047 1621 Dihedral : 5.318 38.345 1304 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 0.78 % Allowed : 5.78 % Favored : 93.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.23), residues: 1167 helix: 0.31 (0.18), residues: 762 sheet: -1.18 (0.48), residues: 73 loop : 0.38 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 216 HIS 0.008 0.002 HIS A 55 PHE 0.023 0.002 PHE A 324 TYR 0.015 0.002 TYR A 985 ARG 0.007 0.001 ARG A1193 *********************** 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 : 1.541 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: A 1092 SER cc_start: 0.8652 (m) cc_final: 0.8345 (m) REVERT: A 1146 LEU cc_start: 0.7527 (mt) cc_final: 0.7290 (mt) REVERT: A 1256 ASP cc_start: 0.8451 (t0) cc_final: 0.8163 (t70) outliers start: 8 outliers final: 8 residues processed: 127 average time/residue: 0.5962 time to fit residues: 103.0345 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 : 1.543 ------------------------------------------------------------------------------- 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 59 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 114 optimal weight: 9.9990 chunk 94 optimal weight: 9.9990 chunk 105 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 HIS A 999 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9616 Z= 0.241 Angle : 0.557 5.601 13029 Z= 0.306 Chirality : 0.038 0.142 1506 Planarity : 0.004 0.045 1621 Dihedral : 5.081 37.991 1304 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 0.98 % Allowed : 7.05 % Favored : 91.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.24), residues: 1167 helix: 0.85 (0.18), residues: 761 sheet: -1.57 (0.46), residues: 75 loop : 0.62 (0.37), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 733 HIS 0.007 0.001 HIS A 153 PHE 0.024 0.002 PHE A 324 TYR 0.009 0.001 TYR A 728 ARG 0.007 0.000 ARG A 503 *********************** 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 124 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 114 time to evaluate : 1.380 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: A 276 MET cc_start: 0.7582 (mmm) cc_final: 0.7197 (mmt) REVERT: A 1256 ASP cc_start: 0.8504 (t0) cc_final: 0.8173 (t70) outliers start: 10 outliers final: 9 residues processed: 122 average time/residue: 0.5806 time to fit residues: 96.6347 Evaluate side-chains 110 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 1.634 ------------------------------------------------------------------------------- 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 237 CYS 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 105 optimal weight: 0.9980 chunk 80 optimal weight: 6.9990 chunk 55 optimal weight: 20.0000 chunk 11 optimal weight: 3.9990 chunk 50 optimal weight: 8.9990 chunk 71 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 113 optimal weight: 8.9990 chunk 101 optimal weight: 0.2980 chunk 30 optimal weight: 1.9990 chunk 94 optimal weight: 8.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9616 Z= 0.216 Angle : 0.530 5.281 13029 Z= 0.289 Chirality : 0.038 0.149 1506 Planarity : 0.004 0.045 1621 Dihedral : 4.893 35.865 1304 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.27 % Allowed : 8.13 % Favored : 90.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.25), residues: 1167 helix: 1.19 (0.19), residues: 756 sheet: -1.59 (0.47), residues: 75 loop : 0.73 (0.37), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 733 HIS 0.006 0.001 HIS A 152 PHE 0.018 0.001 PHE A 336 TYR 0.009 0.001 TYR A 92 ARG 0.006 0.000 ARG A 503 *********************** 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: 13 poor density : 106 time to evaluate : 1.452 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 1256 ASP cc_start: 0.8504 (t0) cc_final: 0.8162 (t70) outliers start: 13 outliers final: 11 residues processed: 116 average time/residue: 0.5204 time to fit residues: 83.9744 Evaluate side-chains 108 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 1.552 ------------------------------------------------------------------------------- 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 199 SER Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 247 LEU 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 64 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 84 optimal weight: 2.9990 chunk 46 optimal weight: 8.9990 chunk 96 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 57 optimal weight: 20.0000 chunk 101 optimal weight: 0.4980 chunk 28 optimal weight: 2.9990 chunk 38 optimal weight: 20.0000 overall best weight: 2.6988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9616 Z= 0.325 Angle : 0.563 5.291 13029 Z= 0.312 Chirality : 0.039 0.146 1506 Planarity : 0.004 0.048 1621 Dihedral : 4.890 37.072 1304 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.57 % Allowed : 8.62 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.24), residues: 1167 helix: 1.07 (0.18), residues: 755 sheet: -1.60 (0.51), residues: 67 loop : 0.57 (0.36), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 733 HIS 0.008 0.002 HIS A 798 PHE 0.022 0.002 PHE A 336 TYR 0.009 0.001 TYR A 339 ARG 0.005 0.001 ARG A 503 *********************** 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 119 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 1.448 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: A 1256 ASP cc_start: 0.8474 (t0) cc_final: 0.8215 (t70) outliers start: 16 outliers final: 13 residues processed: 115 average time/residue: 0.5281 time to fit residues: 85.0424 Evaluate side-chains 113 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 1.602 ------------------------------------------------------------------------------- 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 237 CYS Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 826 SER 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 1119 ILE Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1197 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 101 optimal weight: 0.3980 chunk 22 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 27 optimal weight: 0.4980 chunk 113 optimal weight: 8.9990 chunk 93 optimal weight: 6.9990 chunk 52 optimal weight: 20.0000 chunk 9 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9616 Z= 0.202 Angle : 0.504 5.099 13029 Z= 0.274 Chirality : 0.037 0.146 1506 Planarity : 0.004 0.046 1621 Dihedral : 4.730 37.785 1304 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.27 % Allowed : 8.03 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.25), residues: 1167 helix: 1.45 (0.19), residues: 755 sheet: -1.55 (0.49), residues: 74 loop : 0.71 (0.37), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 733 HIS 0.005 0.001 HIS A 152 PHE 0.019 0.001 PHE A 336 TYR 0.009 0.001 TYR A 92 ARG 0.004 0.000 ARG A 503 *********************** 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 115 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 1.422 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: A 1256 ASP cc_start: 0.8509 (t0) cc_final: 0.8249 (t70) outliers start: 13 outliers final: 10 residues processed: 111 average time/residue: 0.5356 time to fit residues: 83.4063 Evaluate side-chains 106 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 1.451 ------------------------------------------------------------------------------- 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 1015 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 12 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 95 optimal weight: 7.9990 chunk 63 optimal weight: 0.8980 chunk 112 optimal weight: 10.0000 chunk 70 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 52 optimal weight: 30.0000 chunk 69 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3891 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= 0.213 Angle : 0.509 6.168 13029 Z= 0.276 Chirality : 0.037 0.144 1506 Planarity : 0.004 0.045 1621 Dihedral : 4.628 38.238 1304 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.27 % Allowed : 8.23 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.25), residues: 1167 helix: 1.52 (0.19), residues: 756 sheet: -1.56 (0.52), residues: 67 loop : 0.67 (0.36), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 733 HIS 0.006 0.001 HIS A 798 PHE 0.018 0.001 PHE A 336 TYR 0.010 0.001 TYR A1255 ARG 0.009 0.000 ARG A 542 *********************** 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 114 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 1.583 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: A 1256 ASP cc_start: 0.8506 (t0) cc_final: 0.8182 (t70) outliers start: 13 outliers final: 10 residues processed: 109 average time/residue: 0.5676 time to fit residues: 85.8568 Evaluate side-chains 105 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 1.491 ------------------------------------------------------------------------------- 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 1061 LEU Chi-restraints excluded: chain A residue 1092 SER Chi-restraints excluded: chain A residue 1119 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 67 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 55 optimal weight: 30.0000 chunk 10 optimal weight: 3.9990 chunk 88 optimal weight: 0.5980 chunk 102 optimal weight: 10.0000 chunk 108 optimal weight: 10.0000 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.4030 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= 0.192 Angle : 0.498 7.821 13029 Z= 0.268 Chirality : 0.037 0.151 1506 Planarity : 0.003 0.045 1621 Dihedral : 4.599 40.348 1304 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.08 % Allowed : 8.42 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.25), residues: 1167 helix: 1.65 (0.19), residues: 756 sheet: -1.70 (0.51), residues: 67 loop : 0.69 (0.36), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 733 HIS 0.005 0.001 HIS A 152 PHE 0.018 0.001 PHE A 336 TYR 0.013 0.001 TYR A1255 ARG 0.008 0.000 ARG A 542 *********************** 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 112 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 1.524 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 outliers start: 11 outliers final: 10 residues processed: 110 average time/residue: 0.5089 time to fit residues: 79.2333 Evaluate side-chains 107 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 1.510 ------------------------------------------------------------------------------- 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 1061 LEU Chi-restraints excluded: chain A residue 1092 SER Chi-restraints excluded: chain A residue 1102 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 8.9990 chunk 105 optimal weight: 9.9990 chunk 108 optimal weight: 9.9990 chunk 63 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 94 optimal weight: 10.0000 chunk 99 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.4118 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= 0.178 Angle : 0.492 7.846 13029 Z= 0.265 Chirality : 0.037 0.139 1506 Planarity : 0.003 0.045 1621 Dihedral : 4.545 42.229 1304 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.98 % Allowed : 8.81 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.25), residues: 1167 helix: 1.76 (0.19), residues: 755 sheet: -1.73 (0.51), residues: 67 loop : 0.70 (0.36), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 733 HIS 0.005 0.001 HIS A 798 PHE 0.017 0.001 PHE A 336 TYR 0.008 0.001 TYR A1016 ARG 0.009 0.000 ARG A 542 *********************** 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 111 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 1.528 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 241 MET cc_start: 0.7274 (mmm) cc_final: 0.6979 (mmm) REVERT: A 1256 ASP cc_start: 0.8308 (t0) cc_final: 0.8107 (t70) outliers start: 10 outliers final: 10 residues processed: 109 average time/residue: 0.4955 time to fit residues: 77.6733 Evaluate side-chains 110 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 1.531 ------------------------------------------------------------------------------- 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 1061 LEU Chi-restraints excluded: chain A residue 1092 SER Chi-restraints excluded: chain A residue 1102 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 111 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 52 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 116 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 92 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 56 optimal weight: 20.0000 chunk 73 optimal weight: 0.0980 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.4151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9616 Z= 0.279 Angle : 0.528 8.050 13029 Z= 0.288 Chirality : 0.038 0.143 1506 Planarity : 0.004 0.045 1621 Dihedral : 4.606 40.904 1304 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.98 % Allowed : 8.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.25), residues: 1167 helix: 1.54 (0.19), residues: 756 sheet: -1.78 (0.51), residues: 67 loop : 0.63 (0.36), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 733 HIS 0.007 0.001 HIS A 152 PHE 0.020 0.002 PHE A 336 TYR 0.010 0.001 TYR A1255 ARG 0.008 0.000 ARG A 542 ********************** 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 109 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 1.656 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 241 MET cc_start: 0.7251 (mmm) cc_final: 0.7021 (mmm) outliers start: 10 outliers final: 10 residues processed: 107 average time/residue: 0.4926 time to fit residues: 76.0400 Evaluate side-chains 107 residues out of total 1021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 1.555 ------------------------------------------------------------------------------- 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 1061 LEU Chi-restraints excluded: chain A residue 1092 SER Chi-restraints excluded: chain A residue 1102 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 92 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 95 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 = 0.4362 r_free = 0.4362 target = 0.174884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.126634 restraints weight = 45821.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.126826 restraints weight = 20365.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.128056 restraints weight = 14299.320| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.4231 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= 0.274 Angle : 0.526 6.777 13029 Z= 0.289 Chirality : 0.038 0.145 1506 Planarity : 0.004 0.045 1621 Dihedral : 4.644 41.524 1304 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.08 % Allowed : 9.30 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.25), residues: 1167 helix: 1.53 (0.19), residues: 755 sheet: -1.81 (0.52), residues: 67 loop : 0.61 (0.36), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 733 HIS 0.007 0.001 HIS A 798 PHE 0.024 0.002 PHE A 882 TYR 0.008 0.001 TYR A 339 ARG 0.008 0.000 ARG A 542 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3699.67 seconds wall clock time: 67 minutes 1.24 seconds (4021.24 seconds total)