Starting phenix.real_space_refine on Fri Sep 11 16:16:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/3jd8_6640/09_2026/3jd8_6640.cif Found real_map, /net/cci-nas-00/data/ceres_data/3jd8_6640/09_2026/3jd8_6640.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/3jd8_6640/09_2026/3jd8_6640.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/3jd8_6640/09_2026/3jd8_6640.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/3jd8_6640/09_2026/3jd8_6640.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3jd8_6640/09_2026/3jd8_6640.map" model { file = "/net/cci-nas-00/data/ceres_data/3jd8_6640/09_2026/3jd8_6640.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3jd8_6640/09_2026/3jd8_6640.cif" } resolution = 4.43 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2193 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 5075 2.51 5 N 1336 2.21 5 O 1597 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.15s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8050 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 7695 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1133, 7694 Classifications: {'peptide': 1133} Incomplete info: {'truncation_to_alanine': 341} Link IDs: {'CIS': 5, 'PCIS': 3, 'PTRANS': 56, 'TRANS': 1068} Chain breaks: 2 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 1271 Unresolved non-hydrogen angles: 1643 Unresolved non-hydrogen dihedrals: 1110 Unresolved non-hydrogen chiralities: 105 Planarities with less than four sites: {'TRP:plan': 9, 'ASP:plan': 20, 'TYR:plan': 15, 'PHE:plan': 37, 'GLU:plan': 10, 'ARG:plan': 16, 'ASN:plan1': 14, 'HIS:plan': 6, 'GLN:plan1': 14} Unresolved non-hydrogen planarities: 716 Conformer: "B" Number of residues, atoms: 1133, 7694 Classifications: {'peptide': 1133} Incomplete info: {'truncation_to_alanine': 341} Link IDs: {'CIS': 5, 'PCIS': 3, 'PTRANS': 56, 'TRANS': 1068} Chain breaks: 2 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 1271 Unresolved non-hydrogen angles: 1643 Unresolved non-hydrogen dihedrals: 1110 Unresolved non-hydrogen chiralities: 105 Planarities with less than four sites: {'TRP:plan': 9, 'ASP:plan': 20, 'TYR:plan': 15, 'PHE:plan': 37, 'GLU:plan': 10, 'ARG:plan': 16, 'ASN:plan1': 14, 'HIS:plan': 6, 'GLN:plan1': 14} Unresolved non-hydrogen planarities: 716 bond proxies already assigned to first conformer: 7835 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 182 Unusual residues: {'CLR': 1, 'NAG': 11} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 3.16, per 1000 atoms: 0.39 Number of scatterers: 8050 At special positions: 0 Unit cell: (84.9251, 97.9905, 169.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 1597 8.00 N 1336 7.00 C 5075 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 25 " - pdb=" SG CYS A 74 " distance=2.05 Simple disulfide: pdb=" SG CYS A 31 " - pdb=" SG CYS A 42 " distance=2.05 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 109 " distance=2.05 Simple disulfide: pdb=" SG CYS A 75 " - pdb=" SG CYS A 113 " distance=2.06 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 238 " distance=2.04 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 160 " distance=2.04 Simple disulfide: pdb=" SG CYS A 177 " - pdb=" SG CYS A 184 " distance=2.08 Simple disulfide: pdb=" SG CYS A 227 " - pdb=" SG CYS A 243 " distance=1.91 Simple disulfide: pdb=" SG CYS A 240 " - pdb=" SG CYS A 247 " distance=1.79 Simple disulfide: pdb=" SG CYS A 468 " - pdb=" SG CYS A 479 " distance=2.10 Simple disulfide: pdb=" SG CYS A 516 " - pdb=" SG CYS A 533 " distance=2.07 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 Links applied ALPHA1-6 " BMA F 3 " - " MAN F 4 " BETA1-4 " NAG A1318 " - " NAG A1319 " " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " NAG-ASN " NAG A1303 " - " ASN A 158 " " NAG A1309 " - " ASN A 572 " " NAG A1316 " - " ASN A 122 " " NAG A1317 " - " ASN A 70 " " NAG A1319 " - " ASN A 185 " " NAG A1320 " - " ASN A1064 " " NAG A1322 " - " ASN A 135 " " NAG A1324 " - " ASN A 459 " " NAG B 1 " - " ASN A 222 " " NAG C 1 " - " ASN A 524 " " NAG D 1 " - " ASN A 557 " " NAG E 1 " - " ASN A 598 " Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 307.2 milliseconds 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2118 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 7 sheets defined 53.0% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 52 through 54 No H-bonds generated for 'chain 'A' and resid 52 through 54' Processing helix chain 'A' and resid 55 through 63 Processing helix chain 'A' and resid 64 through 67 Processing helix chain 'A' and resid 76 through 86 Processing helix chain 'A' and resid 87 through 95 Processing helix chain 'A' and resid 97 through 114 Processing helix chain 'A' and resid 116 through 119 Processing helix chain 'A' and resid 149 through 161 Processing helix chain 'A' and resid 172 through 177 removed outlier: 3.599A pdb=" N LEU A 176 " --> pdb=" O ALA A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 194 Processing helix chain 'A' and resid 195 through 199 Processing helix chain 'A' and resid 260 through 288 removed outlier: 3.607A pdb=" N GLY A 264 " --> pdb=" O TRP A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 348 Processing helix chain 'A' and resid 351 through 369 Processing helix chain 'A' and resid 387 through 400 Processing helix chain 'A' and resid 432 through 435 Processing helix chain 'A' and resid 436 through 452 Processing helix chain 'A' and resid 464 through 468 Processing helix chain 'A' and resid 483 through 489 Processing helix chain 'A' and resid 491 through 497 Processing helix chain 'A' and resid 510 through 517 Processing helix chain 'A' and resid 542 through 545 Processing helix chain 'A' and resid 554 through 558 Processing helix chain 'A' and resid 573 through 594 removed outlier: 3.534A pdb=" N ARG A 579 " --> pdb=" O GLU A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 617 removed outlier: 4.051A pdb=" N LEU A 613 " --> pdb=" O ILE A 609 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN A 614 " --> pdb=" O GLU A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 638 removed outlier: 3.928A pdb=" N PHE A 622 " --> pdb=" O ASP A 618 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N THR A 623 " --> pdb=" O SER A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 666 removed outlier: 4.228A pdb=" N LEU A 648 " --> pdb=" O SER A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 698 removed outlier: 3.645A pdb=" N ILE A 678 " --> pdb=" O VAL A 674 " (cutoff:3.500A) Proline residue: A 681 - end of helix removed outlier: 4.523A pdb=" N LEU A 684 " --> pdb=" O LEU A 680 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ILE A 685 " --> pdb=" O PRO A 681 " (cutoff:3.500A) Proline residue: A 691 - end of helix removed outlier: 3.797A pdb=" N VAL A 694 " --> pdb=" O ILE A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 714 removed outlier: 3.662A pdb=" N TYR A 709 " --> pdb=" O LEU A 705 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLN A 710 " --> pdb=" O VAL A 706 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASP A 712 " --> pdb=" O ALA A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 732 removed outlier: 3.514A pdb=" N ARG A 726 " --> pdb=" O GLN A 722 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL A 731 " --> pdb=" O VAL A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 772 removed outlier: 3.521A pdb=" N VAL A 753 " --> pdb=" O GLY A 749 " (cutoff:3.500A) Proline residue: A 755 - end of helix removed outlier: 4.352A pdb=" N SER A 761 " --> pdb=" O VAL A 757 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE A 763 " --> pdb=" O THR A 759 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA A 764 " --> pdb=" O PHE A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 830 Proline residue: A 827 - end of helix removed outlier: 3.982A pdb=" N LEU A 830 " --> pdb=" O SER A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 851 Processing helix chain 'A' and resid 864 through 876 Processing helix chain 'A' and resid 987 through 995 removed outlier: 3.527A pdb=" N GLN A 991 " --> pdb=" O LYS A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1005 Processing helix chain 'A' and resid 1047 through 1069 removed outlier: 3.908A pdb=" N MET A1069 " --> pdb=" O VAL A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1089 Processing helix chain 'A' and resid 1090 through 1092 No H-bonds generated for 'chain 'A' and resid 1090 through 1092' Processing helix chain 'A' and resid 1093 through 1113 Processing helix chain 'A' and resid 1122 through 1144 removed outlier: 3.595A pdb=" N THR A1130 " --> pdb=" O ILE A1126 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA A1132 " --> pdb=" O CYS A1128 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU A1135 " --> pdb=" O ILE A1131 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASN A1137 " --> pdb=" O MET A1133 " (cutoff:3.500A) Processing helix chain 'A' and resid 1150 through 1174 removed outlier: 3.828A pdb=" N VAL A1155 " --> pdb=" O ALA A1151 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N HIS A1170 " --> pdb=" O GLU A1166 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE A1171 " --> pdb=" O PHE A1167 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA A1174 " --> pdb=" O HIS A1170 " (cutoff:3.500A) Processing helix chain 'A' and resid 1184 through 1214 removed outlier: 3.760A pdb=" N GLU A1188 " --> pdb=" O VAL A1184 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N HIS A1193 " --> pdb=" O GLU A1189 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER A1196 " --> pdb=" O ALA A1192 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N SER A1197 " --> pdb=" O HIS A1193 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE A1202 " --> pdb=" O VAL A1198 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR A1203 " --> pdb=" O PHE A1199 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL A1211 " --> pdb=" O PHE A1207 " (cutoff:3.500A) Processing sheet with id=A, first strand: chain 'A' and resid 27 through 35 removed outlier: 6.448A pdb=" N GLU A 30 " --> pdb=" O CYS A 42 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N CYS A 42 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLY A 32 " --> pdb=" O TYR A 40 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LYS A 38 " --> pdb=" O ALA A 34 " (cutoff:3.500A) Processing sheet with id=B, first strand: chain 'A' and resid 49 through 50 Processing sheet with id=C, first strand: chain 'A' and resid 121 through 130 removed outlier: 6.931A pdb=" N LEU A 121 " --> pdb=" O TYR A 146 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N TYR A 146 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL A 123 " --> pdb=" O LEU A 144 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU A 144 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ALA A 125 " --> pdb=" O LYS A 142 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N THR A 204 " --> pdb=" O LYS A 142 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 144 " --> pdb=" O THR A 204 " (cutoff:3.500A) Processing sheet with id=D, first strand: chain 'A' and resid 547 through 548 Processing sheet with id=E, first strand: chain 'A' and resid 418 through 419 Processing sheet with id=F, first strand: chain 'A' and resid 454 through 457 Processing sheet with id=G, first strand: chain 'A' and resid 499 through 500 removed outlier: 6.757A pdb=" N LYS A 499 " --> pdb=" O TYR A 506 " (cutoff:3.500A) 420 hydrogen bonds defined for protein. 1206 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.34 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.44: 3489 1.44 - 1.67: 4645 1.67 - 1.90: 60 1.90 - 2.13: 0 2.13 - 2.36: 1 Bond restraints: 8195 Sorted by residual: bond pdb=" C VAL A 959 " pdb=" N PRO A 984 " ideal model delta sigma weight residual 1.334 2.360 -1.026 2.34e-02 1.83e+03 1.92e+03 bond pdb=" C SER A 940 " pdb=" N SER A 941 " ideal model delta sigma weight residual 1.332 1.657 -0.325 1.40e-02 5.10e+03 5.38e+02 bond pdb=" C LEU A 469 " pdb=" N ALA A 470 " ideal model delta sigma weight residual 1.334 1.216 0.118 1.26e-02 6.30e+03 8.77e+01 bond pdb=" C LEU A1060 " pdb=" N ILE A1061 " ideal model delta sigma weight residual 1.334 1.441 -0.107 1.25e-02 6.40e+03 7.33e+01 bond pdb=" C GLN A 881 " pdb=" N TYR A 882 " ideal model delta sigma weight residual 1.331 1.221 0.111 1.33e-02 5.65e+03 6.93e+01 ... (remaining 8190 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.42: 11153 6.42 - 12.84: 59 12.84 - 19.26: 19 19.26 - 25.67: 2 25.67 - 32.09: 1 Bond angle restraints: 11234 Sorted by residual: angle pdb=" CA VAL A 959 " pdb=" C VAL A 959 " pdb=" N PRO A 984 " ideal model delta sigma weight residual 118.88 86.79 32.09 1.54e+00 4.22e-01 4.34e+02 angle pdb=" O VAL A 959 " pdb=" C VAL A 959 " pdb=" N PRO A 984 " ideal model delta sigma weight residual 121.10 143.58 -22.48 1.14e+00 7.69e-01 3.89e+02 angle pdb=" C VAL A 959 " pdb=" N PRO A 984 " pdb=" CA PRO A 984 " ideal model delta sigma weight residual 119.84 98.82 21.02 1.25e+00 6.40e-01 2.83e+02 angle pdb=" N GLN A 881 " pdb=" CA GLN A 881 " pdb=" C GLN A 881 " ideal model delta sigma weight residual 108.86 123.53 -14.67 1.41e+00 5.03e-01 1.08e+02 angle pdb=" N PHE A 995 " pdb=" CA PHE A 995 " pdb=" C PHE A 995 " ideal model delta sigma weight residual 108.34 121.88 -13.54 1.31e+00 5.83e-01 1.07e+02 ... (remaining 11229 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 4205 17.95 - 35.91: 278 35.91 - 53.86: 111 53.86 - 71.82: 45 71.82 - 89.77: 14 Dihedral angle restraints: 4653 sinusoidal: 1370 harmonic: 3283 Sorted by residual: dihedral pdb=" CB CYS A 240 " pdb=" SG CYS A 240 " pdb=" SG CYS A 247 " pdb=" CB CYS A 247 " ideal model delta sinusoidal sigma weight residual 93.00 13.01 79.99 1 1.00e+01 1.00e-02 7.93e+01 dihedral pdb=" C SER A 602 " pdb=" N SER A 602 " pdb=" CA SER A 602 " pdb=" CB SER A 602 " ideal model delta harmonic sigma weight residual -122.60 -102.74 -19.86 0 2.50e+00 1.60e-01 6.31e+01 dihedral pdb=" CA SER A 602 " pdb=" C SER A 602 " pdb=" N PHE A 603 " pdb=" CA PHE A 603 " ideal model delta harmonic sigma weight residual 180.00 -142.67 -37.33 0 5.00e+00 4.00e-02 5.57e+01 ... (remaining 4650 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.409: 1394 0.409 - 0.817: 10 0.817 - 1.226: 4 1.226 - 1.634: 2 1.634 - 2.043: 1 Chirality restraints: 1411 Sorted by residual: chirality pdb=" C1 NAG A1318 " pdb=" C2 NAG A1318 " pdb=" O5 NAG A1318 " pdb=" O4 NAG A1319 " both_signs ideal model delta sigma weight residual False -2.40 -0.84 -1.56 2.00e-02 2.50e+03 6.11e+03 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.87 -1.53 2.00e-02 2.50e+03 5.85e+03 chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-02 2.50e+03 4.95e+02 ... (remaining 1408 not shown) Planarity restraints: 1465 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 572 " 0.132 2.00e-02 2.50e+03 2.94e-01 1.08e+03 pdb=" CG ASN A 572 " -0.081 2.00e-02 2.50e+03 pdb=" OD1 ASN A 572 " 0.155 2.00e-02 2.50e+03 pdb=" ND2 ASN A 572 " -0.530 2.00e-02 2.50e+03 pdb=" C1 NAG A1309 " 0.323 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " -0.329 2.00e-02 2.50e+03 2.85e-01 1.02e+03 pdb=" C7 NAG D 1 " 0.074 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " -0.046 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " 0.501 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " -0.200 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " -0.308 2.00e-02 2.50e+03 2.59e-01 8.41e+02 pdb=" C7 NAG D 2 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " -0.188 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " 0.446 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " -0.030 2.00e-02 2.50e+03 ... (remaining 1462 not shown) Histogram of nonbonded interaction distances: 1.34 - 2.05: 39 2.05 - 2.76: 1317 2.76 - 3.47: 12438 3.47 - 4.19: 18697 4.19 - 4.90: 31124 Nonbonded interactions: 63615 Sorted by model distance: nonbonded pdb=" O TRP A 942 " pdb=" CB CYS A1011 " model vdw 1.335 3.440 nonbonded pdb=" CD2 LEU A 656 " pdb=" CB PRO A 755 " model vdw 1.371 3.860 nonbonded pdb=" CG1 VAL A 727 " pdb=" CG1 VAL A1165 " model vdw 1.411 3.880 nonbonded pdb=" CD2 LEU A 680 " pdb=" CE2 TYR A1229 " model vdw 1.470 3.760 nonbonded pdb=" O LEU A 656 " pdb=" CD1 LEU A 751 " model vdw 1.483 3.460 ... (remaining 63610 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'E' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.300 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6219 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 : 0.021 1.026 8227 Z= 1.084 Angle : 2.156 53.458 11319 Z= 1.152 Chirality : 0.128 2.043 1411 Planarity : 0.016 0.285 1453 Dihedral : 16.872 89.775 2502 Min Nonbonded Distance : 1.335 Molprobity Statistics. All-atom Clashscore : 78.06 Ramachandran Plot: Outliers : 8.36 % Allowed : 11.91 % Favored : 79.73 % Rotamer: Outliers : 11.82 % Allowed : 8.55 % Favored : 79.63 % Cbeta Deviations : 0.47 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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 are not related in a simple way. whole: -3.27 (0.23), residues: 1125 helix: -1.35 (0.20), residues: 546 sheet: -0.69 (0.56), residues: 85 loop : -3.45 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 78 TYR 0.030 0.003 TYR A 147 PHE 0.025 0.003 PHE A 203 TRP 0.021 0.004 TRP A 27 HIS 0.007 0.001 HIS A 441 Details of bonding type rmsd/Z covalent geometry : bond 0.01542 / 0.85 ( 8195) covalent geometry : angle 1.56376 / 1.02 (11234) SS BOND : bond 0.08723 / 4.52 ( 11) SS BOND : angle 14.65505 / 11.42 ( 22) hydrogen bonds : bond 0.22692 / 14.92 ( 420) hydrogen bonds : angle 9.16474 / 6.85 ( 1206) link_ALPHA1-6 : bond 0.00261 / 0.14 ( 1) link_ALPHA1-6 : angle 0.41226 / 0.23 ( 3) link_BETA1-4 : bond 0.06807 / 3.75 ( 8) link_BETA1-4 : angle 12.10249 / 7.59 ( 24) link_NAG-ASN : bond 0.34127 / 19.49 ( 12) link_NAG-ASN : angle 21.66886 / 13.86 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 248 time to evaluate : 0.263 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 38 LYS cc_start: 0.7348 (mttm) cc_final: 0.7017 (mmtm) REVERT: A 467 ILE cc_start: 0.8263 (pt) cc_final: 0.7808 (mm) REVERT: A 523 LEU cc_start: 0.7793 (mt) cc_final: 0.7582 (tp) REVERT: A 541 VAL cc_start: 0.7976 (t) cc_final: 0.7669 (t) REVERT: A 588 ILE cc_start: 0.8360 (mt) cc_final: 0.7486 (tp) REVERT: A 678 ILE cc_start: 0.8283 (mt) cc_final: 0.8069 (mt) REVERT: A 722 GLN cc_start: 0.8864 (OUTLIER) cc_final: 0.8096 (tm-30) REVERT: A 760 PHE cc_start: 0.8994 (OUTLIER) cc_final: 0.8694 (t80) REVERT: A 1048 SER cc_start: 0.4564 (p) cc_final: 0.3996 (p) REVERT: A 1072 ASN cc_start: 0.4586 (OUTLIER) cc_final: 0.3909 (t0) REVERT: A 1094 ILE cc_start: 0.9160 (mm) cc_final: 0.8781 (mm) outliers start: 76 outliers final: 25 residues processed: 290 average time/residue: 0.0891 time to fit residues: 35.1777 Evaluate side-chains 180 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 20.0000 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 106 optimal weight: 9.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 106 ASN A 150 GLN A 154 ASN A 200 GLN ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 GLN ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 HIS ** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.087458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.072442 restraints weight = 49136.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.073500 restraints weight = 38172.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.074273 restraints weight = 31362.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.074891 restraints weight = 26903.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.075355 restraints weight = 23813.474| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3580 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3580 r_free = 0.3580 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3580 r_free = 0.3580 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3580 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6723 moved from start: 0.4436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 8227 Z= 0.269 Angle : 1.225 21.042 11319 Z= 0.573 Chirality : 0.065 0.771 1411 Planarity : 0.006 0.100 1453 Dihedral : 6.399 44.366 1193 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 18.03 Ramachandran Plot: Outliers : 2.04 % Allowed : 9.32 % Favored : 88.64 % Rotamer: Outliers : 0.16 % Allowed : 2.64 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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 are not related in a simple way. whole: -1.72 (0.25), residues: 1127 helix: 0.11 (0.22), residues: 572 sheet: 0.48 (0.62), residues: 66 loop : -3.02 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 161 TYR 0.039 0.003 TYR A 56 PHE 0.051 0.003 PHE A 760 TRP 0.054 0.006 TRP A 381 HIS 0.010 0.002 HIS A1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00575 / 0.27 ( 8195) covalent geometry : angle 1.09766 / 0.54 (11234) SS BOND : bond 0.01049 / 0.47 ( 11) SS BOND : angle 2.48284 / 1.63 ( 22) hydrogen bonds : bond 0.06437 / 4.23 ( 420) hydrogen bonds : angle 5.94208 / 4.45 ( 1206) link_ALPHA1-6 : bond 0.00565 / 0.30 ( 1) link_ALPHA1-6 : angle 1.52995 / 0.86 ( 3) link_BETA1-4 : bond 0.02087 / 1.35 ( 8) link_BETA1-4 : angle 4.30858 / 2.42 ( 24) link_NAG-ASN : bond 0.01188 / 0.78 ( 12) link_NAG-ASN : angle 8.92822 / 6.42 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 193 time to evaluate : 0.302 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: A 106 ASN cc_start: 0.9349 (m-40) cc_final: 0.8859 (m-40) REVERT: A 544 TRP cc_start: 0.8546 (p90) cc_final: 0.8275 (p90) REVERT: A 720 LEU cc_start: 0.9440 (mt) cc_final: 0.9195 (mt) REVERT: A 722 GLN cc_start: 0.9235 (tp40) cc_final: 0.8882 (tm-30) REVERT: A 1097 ASP cc_start: 0.8695 (m-30) cc_final: 0.8292 (m-30) REVERT: A 1156 ASN cc_start: 0.8513 (t0) cc_final: 0.7922 (t0) REVERT: A 1168 CYS cc_start: 0.9247 (m) cc_final: 0.8762 (t) REVERT: A 1170 HIS cc_start: 0.8760 (m90) cc_final: 0.8477 (p-80) REVERT: A 1225 TYR cc_start: 0.6869 (t80) cc_final: 0.6631 (t80) REVERT: A 1232 MET cc_start: 0.7997 (ptt) cc_final: 0.7669 (ptt) outliers start: 1 outliers final: 0 residues processed: 194 average time/residue: 0.0741 time to fit residues: 20.8973 Evaluate side-chains 137 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 25 optimal weight: 30.0000 chunk 83 optimal weight: 20.0000 chunk 22 optimal weight: 20.0000 chunk 87 optimal weight: 20.0000 chunk 105 optimal weight: 4.9990 chunk 86 optimal weight: 0.0980 chunk 26 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 110 optimal weight: 0.0980 chunk 47 optimal weight: 2.9990 chunk 67 optimal weight: 40.0000 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 397 GLN ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 GLN A 478 ASN A 490 ASN ** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.085811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.071197 restraints weight = 50072.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.072212 restraints weight = 38598.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.072982 restraints weight = 31603.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.073593 restraints weight = 27010.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.074009 restraints weight = 23874.240| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3555 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3555 r_free = 0.3555 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3555 r_free = 0.3555 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.3555 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.5508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8227 Z= 0.201 Angle : 1.035 16.593 11319 Z= 0.470 Chirality : 0.053 0.571 1411 Planarity : 0.006 0.088 1453 Dihedral : 5.821 54.915 1193 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 1.51 % Allowed : 9.58 % Favored : 88.91 % Rotamer: Outliers : 0.31 % Allowed : 1.71 % Favored : 97.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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 are not related in a simple way. whole: -1.09 (0.26), residues: 1127 helix: 0.63 (0.22), residues: 580 sheet: -0.18 (0.61), residues: 78 loop : -2.66 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1173 TYR 0.021 0.002 TYR A 594 PHE 0.038 0.002 PHE A 760 TRP 0.033 0.004 TRP A 583 HIS 0.008 0.002 HIS A1170 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.20 ( 8195) covalent geometry : angle 0.95025 / 0.45 (11234) SS BOND : bond 0.00969 / 0.35 ( 11) SS BOND : angle 1.91811 / 1.13 ( 22) hydrogen bonds : bond 0.05131 / 3.32 ( 420) hydrogen bonds : angle 5.32002 / 3.97 ( 1206) link_ALPHA1-6 : bond 0.00069 / 0.04 ( 1) link_ALPHA1-6 : angle 1.31046 / 0.71 ( 3) link_BETA1-4 : bond 0.01568 / 0.91 ( 8) link_BETA1-4 : angle 3.36730 / 2.01 ( 24) link_NAG-ASN : bond 0.00828 / 0.50 ( 12) link_NAG-ASN : angle 6.71706 / 4.86 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 171 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASN cc_start: 0.9130 (m-40) cc_final: 0.8801 (m110) REVERT: A 390 LEU cc_start: 0.9246 (mp) cc_final: 0.8330 (mp) REVERT: A 529 LEU cc_start: 0.8393 (tp) cc_final: 0.8147 (tp) REVERT: A 542 PHE cc_start: 0.8358 (m-80) cc_final: 0.8045 (m-80) REVERT: A 544 TRP cc_start: 0.8656 (p90) cc_final: 0.8220 (p90) REVERT: A 722 GLN cc_start: 0.9252 (tp40) cc_final: 0.8800 (tm-30) REVERT: A 1039 MET cc_start: 0.7852 (ppp) cc_final: 0.7123 (mmm) REVERT: A 1084 PHE cc_start: 0.7970 (p90) cc_final: 0.7675 (p90) REVERT: A 1159 MET cc_start: 0.7945 (tmm) cc_final: 0.7615 (tmm) REVERT: A 1202 ILE cc_start: 0.8654 (mm) cc_final: 0.8205 (mm) REVERT: A 1228 MET cc_start: 0.8129 (ppp) cc_final: 0.7545 (ppp) REVERT: A 1232 MET cc_start: 0.8045 (ptt) cc_final: 0.7317 (ptt) outliers start: 2 outliers final: 0 residues processed: 173 average time/residue: 0.0699 time to fit residues: 17.8734 Evaluate side-chains 134 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 102 optimal weight: 10.0000 chunk 46 optimal weight: 8.9990 chunk 105 optimal weight: 9.9990 chunk 97 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 chunk 59 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 93 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 397 GLN ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.083134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.068368 restraints weight = 51977.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.069432 restraints weight = 40735.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.070111 restraints weight = 33356.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.070649 restraints weight = 28845.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.071090 restraints weight = 25820.861| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3503 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3503 r_free = 0.3503 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3503 r_free = 0.3503 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3503 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.6202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8227 Z= 0.204 Angle : 0.961 14.440 11319 Z= 0.443 Chirality : 0.052 0.457 1411 Planarity : 0.005 0.072 1453 Dihedral : 5.671 59.468 1193 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 1.33 % Allowed : 8.52 % Favored : 90.15 % Rotamer: Outliers : 0.16 % Allowed : 2.02 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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 are not related in a simple way. whole: -0.90 (0.26), residues: 1127 helix: 0.78 (0.22), residues: 588 sheet: -0.70 (0.58), residues: 79 loop : -2.49 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 518 TYR 0.018 0.002 TYR A 102 PHE 0.044 0.002 PHE A 101 TRP 0.052 0.005 TRP A 189 HIS 0.008 0.002 HIS A 398 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.20 ( 8195) covalent geometry : angle 0.88109 / 0.42 (11234) SS BOND : bond 0.00429 / 0.25 ( 11) SS BOND : angle 1.76010 / 1.03 ( 22) hydrogen bonds : bond 0.04818 / 3.08 ( 420) hydrogen bonds : angle 5.27890 / 3.92 ( 1206) link_ALPHA1-6 : bond 0.00737 / 0.39 ( 1) link_ALPHA1-6 : angle 1.76601 / 0.97 ( 3) link_BETA1-4 : bond 0.01458 / 0.75 ( 8) link_BETA1-4 : angle 3.11945 / 1.86 ( 24) link_NAG-ASN : bond 0.00620 / 0.39 ( 12) link_NAG-ASN : angle 6.27545 / 4.33 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 148 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.6941 (mmtm) cc_final: 0.6684 (mmtm) REVERT: A 105 LEU cc_start: 0.9335 (mm) cc_final: 0.9129 (pp) REVERT: A 106 ASN cc_start: 0.8917 (m-40) cc_final: 0.8631 (m-40) REVERT: A 529 LEU cc_start: 0.8630 (tp) cc_final: 0.8388 (tp) REVERT: A 542 PHE cc_start: 0.8464 (m-80) cc_final: 0.8058 (m-80) REVERT: A 544 TRP cc_start: 0.8552 (p90) cc_final: 0.8134 (p90) REVERT: A 722 GLN cc_start: 0.9130 (tp40) cc_final: 0.8831 (tm-30) REVERT: A 1084 PHE cc_start: 0.8049 (p90) cc_final: 0.7721 (p90) REVERT: A 1097 ASP cc_start: 0.8694 (m-30) cc_final: 0.8340 (m-30) REVERT: A 1159 MET cc_start: 0.7975 (tmm) cc_final: 0.7709 (tmm) REVERT: A 1225 TYR cc_start: 0.7039 (t80) cc_final: 0.6818 (t80) outliers start: 1 outliers final: 0 residues processed: 149 average time/residue: 0.0731 time to fit residues: 16.0312 Evaluate side-chains 120 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 99 optimal weight: 0.9990 chunk 85 optimal weight: 9.9990 chunk 101 optimal weight: 1.9990 chunk 29 optimal weight: 20.0000 chunk 28 optimal weight: 8.9990 chunk 110 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 62 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 chunk 77 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 GLN A 200 GLN ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.081788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.067138 restraints weight = 50358.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.068144 restraints weight = 39723.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.068802 restraints weight = 32797.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.069177 restraints weight = 28350.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.069462 restraints weight = 25801.971| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3474 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3474 r_free = 0.3474 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3474 r_free = 0.3474 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3474 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.6713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8227 Z= 0.184 Angle : 0.905 13.570 11319 Z= 0.416 Chirality : 0.049 0.400 1411 Planarity : 0.005 0.064 1453 Dihedral : 5.350 43.347 1193 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 1.33 % Allowed : 8.34 % Favored : 90.33 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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 are not related in a simple way. whole: -0.76 (0.26), residues: 1127 helix: 0.95 (0.22), residues: 592 sheet: -1.56 (0.50), residues: 91 loop : -2.33 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 116 TYR 0.013 0.002 TYR A1225 PHE 0.026 0.002 PHE A 760 TRP 0.035 0.003 TRP A 583 HIS 0.007 0.002 HIS A 398 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.18 ( 8195) covalent geometry : angle 0.84099 / 0.40 (11234) SS BOND : bond 0.00559 / 0.29 ( 11) SS BOND : angle 1.53279 / 0.87 ( 22) hydrogen bonds : bond 0.04486 / 2.89 ( 420) hydrogen bonds : angle 5.18002 / 3.85 ( 1206) link_ALPHA1-6 : bond 0.00140 / 0.07 ( 1) link_ALPHA1-6 : angle 1.50389 / 0.84 ( 3) link_BETA1-4 : bond 0.01362 / 0.76 ( 8) link_BETA1-4 : angle 2.95501 / 1.78 ( 24) link_NAG-ASN : bond 0.00714 / 0.42 ( 12) link_NAG-ASN : angle 5.42265 / 3.81 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.6961 (mmtm) cc_final: 0.6724 (mmtm) REVERT: A 105 LEU cc_start: 0.9311 (mm) cc_final: 0.9108 (pp) REVERT: A 106 ASN cc_start: 0.8944 (m-40) cc_final: 0.8649 (m-40) REVERT: A 529 LEU cc_start: 0.8596 (tp) cc_final: 0.8385 (tp) REVERT: A 542 PHE cc_start: 0.8771 (m-80) cc_final: 0.8239 (m-10) REVERT: A 544 TRP cc_start: 0.8837 (p90) cc_final: 0.8227 (p90) REVERT: A 722 GLN cc_start: 0.9104 (tp40) cc_final: 0.8714 (tm-30) REVERT: A 1081 TYR cc_start: 0.7514 (t80) cc_final: 0.7161 (t80) REVERT: A 1097 ASP cc_start: 0.8812 (m-30) cc_final: 0.8421 (m-30) REVERT: A 1159 MET cc_start: 0.8251 (tmm) cc_final: 0.7858 (tmm) REVERT: A 1225 TYR cc_start: 0.7254 (t80) cc_final: 0.6752 (t80) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.0752 time to fit residues: 15.9677 Evaluate side-chains 116 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 35 optimal weight: 8.9990 chunk 65 optimal weight: 10.0000 chunk 100 optimal weight: 9.9990 chunk 59 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 49 optimal weight: 9.9990 chunk 28 optimal weight: 40.0000 chunk 101 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 17 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 GLN A1137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.076445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.062215 restraints weight = 51189.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.063025 restraints weight = 40831.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.063606 restraints weight = 34321.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.064017 restraints weight = 30225.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.064323 restraints weight = 27549.354| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3358 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.3358 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.7742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 8227 Z= 0.294 Angle : 1.023 12.393 11319 Z= 0.489 Chirality : 0.052 0.379 1411 Planarity : 0.006 0.063 1453 Dihedral : 5.903 34.253 1193 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 19.57 Ramachandran Plot: Outliers : 1.24 % Allowed : 9.23 % Favored : 89.53 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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 are not related in a simple way. whole: -1.25 (0.25), residues: 1127 helix: 0.47 (0.22), residues: 592 sheet: -2.20 (0.45), residues: 91 loop : -2.33 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.002 ARG A 116 TYR 0.024 0.003 TYR A1081 PHE 0.030 0.003 PHE A 101 TRP 0.052 0.005 TRP A 583 HIS 0.010 0.002 HIS A 398 Details of bonding type rmsd/Z covalent geometry : bond 0.00604 / 0.29 ( 8195) covalent geometry : angle 0.96741 / 0.48 (11234) SS BOND : bond 0.00573 / 0.35 ( 11) SS BOND : angle 1.92604 / 1.10 ( 22) hydrogen bonds : bond 0.05208 / 3.42 ( 420) hydrogen bonds : angle 5.55949 / 4.11 ( 1206) link_ALPHA1-6 : bond 0.00311 / 0.16 ( 1) link_ALPHA1-6 : angle 1.42459 / 0.78 ( 3) link_BETA1-4 : bond 0.01379 / 0.72 ( 8) link_BETA1-4 : angle 3.16293 / 1.92 ( 24) link_NAG-ASN : bond 0.00685 / 0.42 ( 12) link_NAG-ASN : angle 5.26358 / 3.66 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.7060 (mmtm) cc_final: 0.6860 (mmtm) REVERT: A 407 GLN cc_start: 0.8351 (tm-30) cc_final: 0.8103 (tm-30) REVERT: A 475 TYR cc_start: 0.7114 (t80) cc_final: 0.6894 (t80) REVERT: A 542 PHE cc_start: 0.9008 (m-80) cc_final: 0.8341 (m-80) REVERT: A 544 TRP cc_start: 0.8912 (p90) cc_final: 0.8262 (p90) REVERT: A 760 PHE cc_start: 0.8952 (m-80) cc_final: 0.7941 (t80) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.0745 time to fit residues: 14.0681 Evaluate side-chains 98 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 14 optimal weight: 0.6980 chunk 7 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 chunk 108 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 83 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 486 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.078626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.063910 restraints weight = 52269.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.065047 restraints weight = 38768.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.065803 restraints weight = 31015.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.066376 restraints weight = 26293.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.066814 restraints weight = 23167.497| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3406 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3406 r_free = 0.3406 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3406 r_free = 0.3406 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3406 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.7947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8227 Z= 0.186 Angle : 0.916 12.681 11319 Z= 0.423 Chirality : 0.050 0.357 1411 Planarity : 0.005 0.060 1453 Dihedral : 5.505 32.466 1193 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 1.06 % Allowed : 9.14 % Favored : 89.80 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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 are not related in a simple way. whole: -1.04 (0.26), residues: 1127 helix: 0.67 (0.22), residues: 597 sheet: -2.04 (0.47), residues: 91 loop : -2.33 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 116 TYR 0.019 0.002 TYR A1081 PHE 0.019 0.002 PHE A 603 TRP 0.018 0.002 TRP A 583 HIS 0.007 0.001 HIS A1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.18 ( 8195) covalent geometry : angle 0.86075 / 0.41 (11234) SS BOND : bond 0.00753 / 0.41 ( 11) SS BOND : angle 1.70483 / 1.04 ( 22) hydrogen bonds : bond 0.04592 / 2.98 ( 420) hydrogen bonds : angle 5.17746 / 3.86 ( 1206) link_ALPHA1-6 : bond 0.00466 / 0.25 ( 1) link_ALPHA1-6 : angle 1.45628 / 0.81 ( 3) link_BETA1-4 : bond 0.01304 / 0.71 ( 8) link_BETA1-4 : angle 2.78750 / 1.70 ( 24) link_NAG-ASN : bond 0.00701 / 0.42 ( 12) link_NAG-ASN : angle 5.06798 / 3.53 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 542 PHE cc_start: 0.9024 (m-80) cc_final: 0.8419 (m-80) REVERT: A 544 TRP cc_start: 0.9009 (p90) cc_final: 0.8147 (p90) REVERT: A 586 GLU cc_start: 0.8319 (tp30) cc_final: 0.7985 (tp30) REVERT: A 1101 ASN cc_start: 0.8868 (m-40) cc_final: 0.8511 (m110) REVERT: A 1159 MET cc_start: 0.8198 (ppp) cc_final: 0.7927 (ppp) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.0692 time to fit residues: 12.2997 Evaluate side-chains 100 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 21 optimal weight: 30.0000 chunk 11 optimal weight: 10.0000 chunk 49 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 111 optimal weight: 6.9990 chunk 87 optimal weight: 20.0000 chunk 41 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 65 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 ASN A 145 GLN ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.076555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.061946 restraints weight = 52095.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.063013 restraints weight = 38968.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.063776 restraints weight = 31363.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.064313 restraints weight = 26642.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.064687 restraints weight = 23636.252| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3370 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3370 r_free = 0.3370 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3370 r_free = 0.3370 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3370 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.8472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 8227 Z= 0.222 Angle : 0.934 12.732 11319 Z= 0.435 Chirality : 0.049 0.348 1411 Planarity : 0.005 0.059 1453 Dihedral : 5.444 30.735 1193 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.89 % Allowed : 10.29 % Favored : 88.82 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 are not related in a simple way. whole: -1.07 (0.26), residues: 1127 helix: 0.73 (0.22), residues: 587 sheet: -2.17 (0.48), residues: 95 loop : -2.38 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 389 TYR 0.021 0.002 TYR A1081 PHE 0.024 0.002 PHE A 760 TRP 0.025 0.003 TRP A 583 HIS 0.007 0.002 HIS A1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.22 ( 8195) covalent geometry : angle 0.88014 / 0.42 (11234) SS BOND : bond 0.00441 / 0.27 ( 11) SS BOND : angle 1.60079 / 0.91 ( 22) hydrogen bonds : bond 0.04664 / 3.02 ( 420) hydrogen bonds : angle 5.22986 / 3.88 ( 1206) link_ALPHA1-6 : bond 0.00420 / 0.22 ( 1) link_ALPHA1-6 : angle 1.43044 / 0.79 ( 3) link_BETA1-4 : bond 0.01291 / 0.71 ( 8) link_BETA1-4 : angle 2.84384 / 1.74 ( 24) link_NAG-ASN : bond 0.00720 / 0.42 ( 12) link_NAG-ASN : angle 5.02391 / 3.50 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 542 PHE cc_start: 0.9199 (m-80) cc_final: 0.8557 (m-80) REVERT: A 544 TRP cc_start: 0.8914 (p90) cc_final: 0.8091 (p90) REVERT: A 586 GLU cc_start: 0.8408 (tp30) cc_final: 0.7937 (tp30) REVERT: A 1157 LEU cc_start: 0.8897 (mm) cc_final: 0.8667 (mm) REVERT: A 1163 ILE cc_start: 0.8955 (tt) cc_final: 0.8683 (tt) REVERT: A 1230 LEU cc_start: 0.8798 (tt) cc_final: 0.8473 (tp) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.0742 time to fit residues: 12.7169 Evaluate side-chains 99 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 40 optimal weight: 7.9990 chunk 57 optimal weight: 0.0040 chunk 32 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 72 optimal weight: 30.0000 chunk 71 optimal weight: 20.0000 chunk 87 optimal weight: 30.0000 chunk 16 optimal weight: 7.9990 chunk 1 optimal weight: 20.0000 chunk 84 optimal weight: 30.0000 chunk 43 optimal weight: 8.9990 overall best weight: 5.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 ASN A 200 GLN ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 GLN A1156 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.075913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.061541 restraints weight = 51108.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.062570 restraints weight = 38696.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.063314 restraints weight = 31121.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.063674 restraints weight = 26515.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.064133 restraints weight = 24062.523| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3357 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3357 r_free = 0.3357 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3357 r_free = 0.3357 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3357 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.8825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 8227 Z= 0.231 Angle : 0.947 12.694 11319 Z= 0.441 Chirality : 0.051 0.379 1411 Planarity : 0.005 0.060 1453 Dihedral : 5.515 34.483 1193 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 18.90 Ramachandran Plot: Outliers : 0.89 % Allowed : 9.14 % Favored : 89.97 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 are not related in a simple way. whole: -1.18 (0.26), residues: 1127 helix: 0.62 (0.22), residues: 578 sheet: -2.25 (0.48), residues: 95 loop : -2.34 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 389 TYR 0.019 0.002 TYR A1041 PHE 0.025 0.002 PHE A 108 TRP 0.019 0.003 TRP A 583 HIS 0.008 0.002 HIS A 398 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.23 ( 8195) covalent geometry : angle 0.89380 / 0.43 (11234) SS BOND : bond 0.00418 / 0.27 ( 11) SS BOND : angle 1.46520 / 0.83 ( 22) hydrogen bonds : bond 0.04864 / 3.24 ( 420) hydrogen bonds : angle 5.25904 / 3.90 ( 1206) link_ALPHA1-6 : bond 0.00409 / 0.22 ( 1) link_ALPHA1-6 : angle 1.49769 / 0.83 ( 3) link_BETA1-4 : bond 0.01198 / 0.65 ( 8) link_BETA1-4 : angle 2.81224 / 1.73 ( 24) link_NAG-ASN : bond 0.01014 / 0.60 ( 12) link_NAG-ASN : angle 5.08529 / 3.51 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 475 TYR cc_start: 0.7325 (t80) cc_final: 0.7021 (t80) REVERT: A 544 TRP cc_start: 0.8873 (p90) cc_final: 0.8006 (p90) REVERT: A 586 GLU cc_start: 0.8417 (tp30) cc_final: 0.8168 (tp30) REVERT: A 1101 ASN cc_start: 0.8612 (m110) cc_final: 0.8152 (m110) REVERT: A 1137 ASN cc_start: 0.9373 (m110) cc_final: 0.9030 (m-40) REVERT: A 1163 ILE cc_start: 0.8968 (tt) cc_final: 0.8682 (tt) REVERT: A 1230 LEU cc_start: 0.8817 (tt) cc_final: 0.8547 (tp) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.0705 time to fit residues: 11.5694 Evaluate side-chains 95 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 2 optimal weight: 9.9990 chunk 108 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 112 optimal weight: 20.0000 chunk 87 optimal weight: 30.0000 chunk 14 optimal weight: 4.9990 chunk 48 optimal weight: 9.9990 chunk 66 optimal weight: 0.9980 chunk 53 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.077660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.063199 restraints weight = 52762.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.064314 restraints weight = 39313.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.065079 restraints weight = 31344.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.065430 restraints weight = 26519.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.065975 restraints weight = 23720.939| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3381 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3381 r_free = 0.3381 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3381 r_free = 0.3381 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3381 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.8998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 8227 Z= 0.179 Angle : 0.892 12.812 11319 Z= 0.412 Chirality : 0.049 0.322 1411 Planarity : 0.005 0.059 1453 Dihedral : 5.298 32.443 1193 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.89 % Allowed : 9.32 % Favored : 89.80 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 are not related in a simple way. whole: -1.07 (0.26), residues: 1127 helix: 0.74 (0.22), residues: 585 sheet: -2.21 (0.50), residues: 95 loop : -2.37 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 518 TYR 0.027 0.002 TYR A 628 PHE 0.019 0.002 PHE A 760 TRP 0.020 0.002 TRP A 544 HIS 0.007 0.002 HIS A1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.18 ( 8195) covalent geometry : angle 0.84040 / 0.40 (11234) SS BOND : bond 0.00340 / 0.21 ( 11) SS BOND : angle 1.31579 / 0.73 ( 22) hydrogen bonds : bond 0.04391 / 2.87 ( 420) hydrogen bonds : angle 5.05964 / 3.75 ( 1206) link_ALPHA1-6 : bond 0.00514 / 0.27 ( 1) link_ALPHA1-6 : angle 1.47422 / 0.83 ( 3) link_BETA1-4 : bond 0.01133 / 0.61 ( 8) link_BETA1-4 : angle 2.68359 / 1.64 ( 24) link_NAG-ASN : bond 0.00861 / 0.49 ( 12) link_NAG-ASN : angle 4.89439 / 3.44 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: A 106 ASN cc_start: 0.9336 (p0) cc_final: 0.9047 (p0) REVERT: A 475 TYR cc_start: 0.7227 (t80) cc_final: 0.6974 (t80) REVERT: A 542 PHE cc_start: 0.8989 (m-80) cc_final: 0.8564 (m-10) REVERT: A 544 TRP cc_start: 0.8821 (p90) cc_final: 0.7988 (p90) REVERT: A 586 GLU cc_start: 0.8247 (tp30) cc_final: 0.7936 (tp30) REVERT: A 726 ARG cc_start: 0.9116 (mmp80) cc_final: 0.8530 (mmp80) REVERT: A 1101 ASN cc_start: 0.8520 (m110) cc_final: 0.8222 (m110) REVERT: A 1128 CYS cc_start: 0.8849 (m) cc_final: 0.8294 (m) REVERT: A 1137 ASN cc_start: 0.9373 (m110) cc_final: 0.8946 (m110) REVERT: A 1163 ILE cc_start: 0.8989 (tt) cc_final: 0.8768 (tt) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.0745 time to fit residues: 12.7276 Evaluate side-chains 97 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 44 optimal weight: 0.2980 chunk 83 optimal weight: 4.9990 chunk 64 optimal weight: 40.0000 chunk 23 optimal weight: 0.6980 chunk 43 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 82 optimal weight: 8.9990 chunk 70 optimal weight: 0.0670 chunk 100 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.079193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.064762 restraints weight = 50897.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.065876 restraints weight = 38458.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.066443 restraints weight = 30751.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.067084 restraints weight = 26737.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.067437 restraints weight = 23594.119| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3430 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3430 r_free = 0.3430 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3430 r_free = 0.3430 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3430 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.9085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 8227 Z= 0.146 Angle : 0.849 13.011 11319 Z= 0.388 Chirality : 0.048 0.315 1411 Planarity : 0.004 0.060 1453 Dihedral : 4.970 31.028 1193 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.89 % Allowed : 7.36 % Favored : 91.75 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 are not related in a simple way. whole: -0.96 (0.26), residues: 1127 helix: 0.74 (0.22), residues: 604 sheet: -2.12 (0.50), residues: 91 loop : -2.31 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 116 TYR 0.016 0.002 TYR A1091 PHE 0.019 0.001 PHE A 101 TRP 0.008 0.001 TRP A 583 HIS 0.004 0.001 HIS A1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 ( 8195) covalent geometry : angle 0.79795 / 0.38 (11234) SS BOND : bond 0.00344 / 0.21 ( 11) SS BOND : angle 1.12562 / 0.64 ( 22) hydrogen bonds : bond 0.04122 / 2.73 ( 420) hydrogen bonds : angle 4.83706 / 3.60 ( 1206) link_ALPHA1-6 : bond 0.00599 / 0.32 ( 1) link_ALPHA1-6 : angle 1.47778 / 0.83 ( 3) link_BETA1-4 : bond 0.01177 / 0.66 ( 8) link_BETA1-4 : angle 2.58887 / 1.58 ( 24) link_NAG-ASN : bond 0.00912 / 0.52 ( 12) link_NAG-ASN : angle 4.77091 / 3.34 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1540.12 seconds wall clock time: 27 minutes 19.33 seconds (1639.33 seconds total)