Starting phenix.real_space_refine on Fri Sep 27 10:30:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w5s_21546/09_2024/6w5s_21546.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w5s_21546/09_2024/6w5s_21546.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w5s_21546/09_2024/6w5s_21546.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w5s_21546/09_2024/6w5s_21546.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w5s_21546/09_2024/6w5s_21546.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w5s_21546/09_2024/6w5s_21546.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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 6691 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 75 5.16 5 C 6276 2.51 5 N 1534 2.21 5 O 1814 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 9700 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9360 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1194, 9338 Classifications: {'peptide': 1194} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 62, 'TRANS': 1130} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 1194, 9338 Classifications: {'peptide': 1194} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 62, 'TRANS': 1130} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 9558 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 206 Unusual residues: {'CLR': 1, 'NAG': 9, 'POV': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AARG A 579 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 579 " occ=0.50 residue: pdb=" N AARG A1032 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A1032 " occ=0.50 Time building chain proxies: 9.97, per 1000 atoms: 1.03 Number of scatterers: 9700 At special positions: 0 Unit cell: (101.374, 88.006, 157.074, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 75 16.00 P 1 15.00 O 1814 8.00 N 1534 7.00 C 6276 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 25 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 31 " - pdb=" SG CYS A 42 " distance=2.03 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 109 " distance=2.03 Simple disulfide: pdb=" SG CYS A 75 " - pdb=" SG CYS A 113 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 238 " distance=2.03 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 160 " distance=2.03 Simple disulfide: pdb=" SG CYS A 177 " - pdb=" SG CYS A 184 " distance=2.03 Simple disulfide: pdb=" SG CYS A 227 " - pdb=" SG CYS A 243 " distance=2.03 Simple disulfide: pdb=" SG CYS A 240 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 468 " - pdb=" SG CYS A 479 " distance=2.03 Simple disulfide: pdb=" SG CYS A 516 " - pdb=" SG CYS A 533 " distance=2.02 Simple disulfide: pdb=" SG CYS A 909 " - pdb=" SG CYS A 914 " distance=2.02 Simple disulfide: pdb=" SG CYS A 956 " - pdb=" SG CYS A1011 " distance=2.03 Simple disulfide: pdb=" SG CYS A 957 " - pdb=" SG CYS A 979 " distance=2.03 Simple disulfide: pdb=" SG CYS A 967 " - pdb=" SG CYS A 976 " distance=2.03 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 ALPHA1-3 " NAG C 2 " - " MAN C 3 " ALPHA1-4 " NAG D 2 " - " MAN D 3 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A1401 " - " ASN A 452 " " NAG A1402 " - " ASN A 459 " " NAG A1405 " - " ASN A 524 " " NAG A1409 " - " ASN A 598 " " NAG A1410 " - " ASN A 916 " " NAG A1414 " - " ASN A 961 " " NAG A1415 " - " ASN A 968 " " NAG A1416 " - " ASN A1064 " " NAG A1419 " - " ASN A 158 " " NAG B 1 " - " ASN A 478 " " NAG C 1 " - " ASN A 557 " " NAG D 1 " - " ASN A 931 " " NAG E 1 " - " ASN A 222 " Time building additional restraints: 2.61 Conformation dependent library (CDL) restraints added in 2.3 seconds 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2242 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 7 sheets defined 58.9% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 55 through 63 removed outlier: 3.693A pdb=" N CYS A 63 " --> pdb=" O VAL A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 67 Processing helix chain 'A' and resid 76 through 87 removed outlier: 3.900A pdb=" N THR A 82 " --> pdb=" O ARG A 78 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP A 85 " --> pdb=" O GLN A 81 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN A 86 " --> pdb=" O THR A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 95 Processing helix chain 'A' and resid 97 through 114 removed outlier: 3.897A pdb=" N ASN A 103 " --> pdb=" O SER A 99 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLU A 110 " --> pdb=" O ASN A 106 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU A 111 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER A 114 " --> pdb=" O GLU A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 119 Processing helix chain 'A' and resid 149 through 161 removed outlier: 3.675A pdb=" N ALA A 155 " --> pdb=" O SER A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 176 Processing helix chain 'A' and resid 185 through 195 removed outlier: 3.735A pdb=" N TRP A 189 " --> pdb=" O ASN A 185 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ILE A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 199 Processing helix chain 'A' and resid 268 through 291 removed outlier: 3.539A pdb=" N TRP A 273 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA A 278 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA A 286 " --> pdb=" O VAL A 282 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE A 287 " --> pdb=" O PHE A 283 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE A 288 " --> pdb=" O PHE A 284 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA A 289 " --> pdb=" O GLY A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 349 removed outlier: 3.785A pdb=" N CYS A 334 " --> pdb=" O ALA A 330 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU A 335 " --> pdb=" O PHE A 331 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ARG A 336 " --> pdb=" O GLU A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 366 Processing helix chain 'A' and resid 367 through 371 Processing helix chain 'A' and resid 376 through 382 Processing helix chain 'A' and resid 386 through 399 Processing helix chain 'A' and resid 436 through 453 removed outlier: 3.711A pdb=" N ILE A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 468 Processing helix chain 'A' and resid 483 through 488 removed outlier: 3.574A pdb=" N TYR A 487 " --> pdb=" O VAL A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 497 Processing helix chain 'A' and resid 508 through 519 removed outlier: 3.661A pdb=" N ARG A 518 " --> pdb=" O LEU A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 546 removed outlier: 3.615A pdb=" N VAL A 546 " --> pdb=" O PHE A 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 542 through 546' Processing helix chain 'A' and resid 554 through 558 Processing helix chain 'A' and resid 574 through 593 removed outlier: 3.671A pdb=" N GLU A 586 " --> pdb=" O ALA A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 617 removed outlier: 3.694A pdb=" N ASP A 611 " --> pdb=" O ARG A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 639 removed outlier: 3.642A pdb=" N ILE A 626 " --> pdb=" O PHE A 622 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 639 " --> pdb=" O ILE A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 679 Processing helix chain 'A' and resid 685 through 711 Proline residue: A 691 - end of helix Processing helix chain 'A' and resid 719 through 750 Proline residue: A 733 - end of helix Processing helix chain 'A' and resid 754 through 792 removed outlier: 3.636A pdb=" N THR A 759 " --> pdb=" O PRO A 755 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL A 780 " --> pdb=" O ILE A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 824 removed outlier: 3.525A pdb=" N ASN A 823 " --> pdb=" O ARG A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 824 through 830 removed outlier: 3.895A pdb=" N LEU A 828 " --> pdb=" O SER A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 852 Processing helix chain 'A' and resid 853 through 856 Processing helix chain 'A' and resid 870 through 883 removed outlier: 4.213A pdb=" N ASP A 874 " --> pdb=" O SER A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 907 Processing helix chain 'A' and resid 918 through 930 Processing helix chain 'A' and resid 942 through 951 Processing helix chain 'A' and resid 983 through 988 removed outlier: 4.302A pdb=" N GLN A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 1005 removed outlier: 4.318A pdb=" N MET A 996 " --> pdb=" O GLY A 992 " (cutoff:3.500A) Proline residue: A1000 - end of helix Processing helix chain 'A' and resid 1028 through 1031 Processing helix chain 'A' and resid 1047 through 1070 removed outlier: 3.698A pdb=" N GLY A1070 " --> pdb=" O THR A1066 " (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 1117 Processing helix chain 'A' and resid 1120 through 1146 Processing helix chain 'A' and resid 1152 through 1177 removed outlier: 4.147A pdb=" N GLY A1162 " --> pdb=" O VAL A1158 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE A1163 " --> pdb=" O MET A1159 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL A1165 " --> pdb=" O CYS A1161 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU A1166 " --> pdb=" O GLY A1162 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N HIS A1170 " --> pdb=" O GLU A1166 " (cutoff:3.500A) Processing helix chain 'A' and resid 1182 through 1202 removed outlier: 4.018A pdb=" N SER A1197 " --> pdb=" O HIS A1193 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE A1202 " --> pdb=" O VAL A1198 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1214 Processing helix chain 'A' and resid 1218 through 1225 Processing helix chain 'A' and resid 1225 through 1252 Proline residue: A1245 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.524A pdb=" N CYS A 42 " --> pdb=" O TYR A 28 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 121 through 125 removed outlier: 6.247A pdb=" N LEU A 121 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N TYR A 147 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N VAL A 123 " --> pdb=" O GLN A 145 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N GLN A 145 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU A 144 " --> pdb=" O THR A 206 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N VAL A 208 " --> pdb=" O LEU A 144 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N TYR A 146 " --> pdb=" O VAL A 208 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 128 through 129 Processing sheet with id=AA4, first strand: chain 'A' and resid 547 through 548 Processing sheet with id=AA5, first strand: chain 'A' and resid 418 through 420 Processing sheet with id=AA6, first strand: chain 'A' and resid 1023 through 1025 removed outlier: 5.889A pdb=" N ASN A1024 " --> pdb=" O GLY A1034 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 958 through 959 483 hydrogen bonds defined for protein. 1387 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: 3.03 Time building geometry restraints manager: 3.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3004 1.34 - 1.46: 2507 1.46 - 1.59: 4330 1.59 - 1.71: 2 1.71 - 1.84: 105 Bond restraints: 9948 Sorted by residual: bond pdb=" C31 POV A1421 " pdb=" O31 POV A1421 " ideal model delta sigma weight residual 1.327 1.452 -0.125 2.00e-02 2.50e+03 3.88e+01 bond pdb=" C21 POV A1421 " pdb=" O21 POV A1421 " ideal model delta sigma weight residual 1.330 1.453 -0.123 2.00e-02 2.50e+03 3.78e+01 bond pdb=" C1 NAG A1410 " pdb=" O5 NAG A1410 " ideal model delta sigma weight residual 1.406 1.471 -0.065 2.00e-02 2.50e+03 1.04e+01 bond pdb=" C1 NAG A1405 " pdb=" O5 NAG A1405 " ideal model delta sigma weight residual 1.406 1.465 -0.059 2.00e-02 2.50e+03 8.70e+00 bond pdb=" O12 POV A1421 " pdb=" P POV A1421 " ideal model delta sigma weight residual 1.657 1.608 0.049 2.00e-02 2.50e+03 6.03e+00 ... (remaining 9943 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.95: 13508 4.95 - 9.90: 34 9.90 - 14.84: 0 14.84 - 19.79: 0 19.79 - 24.74: 1 Bond angle restraints: 13543 Sorted by residual: angle pdb=" N ASN A 70 " pdb=" CA ASN A 70 " pdb=" C ASN A 70 " ideal model delta sigma weight residual 110.80 86.06 24.74 2.13e+00 2.20e-01 1.35e+02 angle pdb=" N LYS A 142 " pdb=" CA LYS A 142 " pdb=" C LYS A 142 " ideal model delta sigma weight residual 111.14 118.85 -7.71 1.08e+00 8.57e-01 5.10e+01 angle pdb=" N LYS A 822 " pdb=" CA LYS A 822 " pdb=" C LYS A 822 " ideal model delta sigma weight residual 111.36 118.57 -7.21 1.09e+00 8.42e-01 4.38e+01 angle pdb=" C ASN A 70 " pdb=" N VAL A 71 " pdb=" CA VAL A 71 " ideal model delta sigma weight residual 120.56 113.02 7.54 1.26e+00 6.30e-01 3.58e+01 angle pdb=" N SER A 863 " pdb=" CA SER A 863 " pdb=" C SER A 863 " ideal model delta sigma weight residual 113.97 107.18 6.79 1.28e+00 6.10e-01 2.81e+01 ... (remaining 13538 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.93: 5981 35.93 - 71.86: 166 71.86 - 107.80: 24 107.80 - 143.73: 21 143.73 - 179.66: 2 Dihedral angle restraints: 6194 sinusoidal: 2706 harmonic: 3488 Sorted by residual: dihedral pdb=" CD BARG A 579 " pdb=" NE BARG A 579 " pdb=" CZ BARG A 579 " pdb=" NH1BARG A 579 " ideal model delta sinusoidal sigma weight residual 0.00 -179.66 179.66 1 1.00e+01 1.00e-02 1.92e+02 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 -86.00 1.75 -87.75 1 1.00e+01 1.00e-02 9.22e+01 dihedral pdb=" CB CYS A 909 " pdb=" SG CYS A 909 " pdb=" SG CYS A 914 " pdb=" CB CYS A 914 " ideal model delta sinusoidal sigma weight residual -86.00 -14.78 -71.22 1 1.00e+01 1.00e-02 6.51e+01 ... (remaining 6191 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.939: 1575 0.939 - 1.877: 0 1.877 - 2.816: 0 2.816 - 3.755: 0 3.755 - 4.694: 1 Chirality restraints: 1576 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 2.29 -4.69 2.00e-02 2.50e+03 5.51e+04 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-02 2.50e+03 4.10e+02 chirality pdb=" C1 MAN C 3 " pdb=" O3 NAG C 2 " pdb=" C2 MAN C 3 " pdb=" O5 MAN C 3 " both_signs ideal model delta sigma weight residual False 2.40 2.18 0.22 2.00e-02 2.50e+03 1.22e+02 ... (remaining 1573 not shown) Planarity restraints: 1711 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " -0.351 2.00e-02 2.50e+03 3.03e-01 1.15e+03 pdb=" C7 NAG E 2 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " -0.084 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " 0.537 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " -0.184 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " -0.339 2.00e-02 2.50e+03 2.92e-01 1.07e+03 pdb=" C7 NAG D 2 " 0.078 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " -0.044 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " 0.511 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " -0.207 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 2 " 0.264 2.00e-02 2.50e+03 2.19e-01 6.01e+02 pdb=" C7 NAG B 2 " -0.072 2.00e-02 2.50e+03 pdb=" C8 NAG B 2 " 0.181 2.00e-02 2.50e+03 pdb=" N2 NAG B 2 " -0.365 2.00e-02 2.50e+03 pdb=" O7 NAG B 2 " -0.008 2.00e-02 2.50e+03 ... (remaining 1708 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 74 2.54 - 3.13: 8226 3.13 - 3.72: 14433 3.72 - 4.31: 21333 4.31 - 4.90: 35516 Nonbonded interactions: 79582 Sorted by model distance: nonbonded pdb=" OE2 GLU A 164 " pdb=" NE2 GLN A 241 " model vdw 1.946 3.120 nonbonded pdb=" O PHE A 821 " pdb=" OG SER A 826 " model vdw 2.026 3.040 nonbonded pdb=" O GLN A 119 " pdb=" SD MET A 217 " model vdw 2.032 3.400 nonbonded pdb=" NH2 ARG A 78 " pdb=" OE1 GLN A 81 " model vdw 2.055 3.120 nonbonded pdb=" O CYS A 909 " pdb=" OG SER A 918 " model vdw 2.066 3.040 ... (remaining 79577 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 'E' } ncs_group { reference = chain 'C' selection = chain 'D' } 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 individual isotropic 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: 0.010 Normalize map: mean=0, sd=1: 1.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.000 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 29.990 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.060 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:13.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.125 9948 Z= 0.331 Angle : 0.829 24.740 13543 Z= 0.469 Chirality : 0.129 4.694 1576 Planarity : 0.013 0.303 1698 Dihedral : 18.493 179.661 3907 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 31.03 Ramachandran Plot: Outliers : 0.42 % Allowed : 7.58 % Favored : 92.00 % Rotamer: Outliers : 2.70 % Allowed : 3.67 % Favored : 93.63 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.24 (0.22), residues: 1194 helix: -1.31 (0.19), residues: 626 sheet: -1.98 (0.56), residues: 88 loop : -3.30 (0.24), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 949 HIS 0.006 0.001 HIS A1042 PHE 0.012 0.001 PHE A1079 TYR 0.013 0.001 TYR A 570 ARG 0.002 0.000 ARG A 372 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 151 time to evaluate : 1.090 Fit side-chains REVERT: A 156 MET cc_start: 0.8738 (ttt) cc_final: 0.8538 (ttm) REVERT: A 233 GLU cc_start: 0.7428 (mp0) cc_final: 0.6874 (pm20) REVERT: A 260 TRP cc_start: 0.6129 (m-10) cc_final: 0.5482 (m-90) REVERT: A 586 GLU cc_start: 0.6921 (tp30) cc_final: 0.6641 (tp30) REVERT: A 822 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8387 (tttp) REVERT: A 1158 VAL cc_start: 0.9175 (t) cc_final: 0.8971 (t) outliers start: 27 outliers final: 10 residues processed: 173 average time/residue: 1.1521 time to fit residues: 215.3254 Evaluate side-chains 118 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 107 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 575 GLU Chi-restraints excluded: chain A residue 711 ARG Chi-restraints excluded: chain A residue 822 LYS Chi-restraints excluded: chain A residue 862 GLN Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain A residue 1161 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 0.7980 chunk 90 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 108 optimal weight: 0.0970 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 88 GLN A 92 GLN A 103 ASN A 122 ASN A 136 GLN ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 387 GLN A 553 GLN ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 707 GLN ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 793 ASN A 906 ASN ** A1008 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1016 HIS A1046 GLN A1137 ASN A1193 HIS A1239 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9948 Z= 0.255 Angle : 0.832 13.433 13543 Z= 0.392 Chirality : 0.049 0.311 1576 Planarity : 0.005 0.044 1698 Dihedral : 17.441 176.267 1821 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.57 % Favored : 93.18 % Rotamer: Outliers : 2.51 % Allowed : 11.68 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.23), residues: 1194 helix: -0.16 (0.20), residues: 638 sheet: -1.56 (0.55), residues: 88 loop : -2.54 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 273 HIS 0.009 0.001 HIS A1042 PHE 0.014 0.002 PHE A1224 TYR 0.022 0.002 TYR A 570 ARG 0.004 0.001 ARG A 989 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 111 time to evaluate : 0.983 Fit side-chains revert: symmetry clash REVERT: A 260 TRP cc_start: 0.5724 (m-10) cc_final: 0.5136 (m-90) REVERT: A 288 PHE cc_start: 0.6853 (m-10) cc_final: 0.5990 (OUTLIER) REVERT: A 498 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8369 (ptmt) REVERT: A 586 GLU cc_start: 0.6832 (tp30) cc_final: 0.6523 (tp30) REVERT: A 862 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.7886 (pt0) outliers start: 25 outliers final: 13 residues processed: 127 average time/residue: 1.0242 time to fit residues: 141.6072 Evaluate side-chains 105 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 91 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 688 GLU Chi-restraints excluded: chain A residue 862 GLN Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1114 MET Chi-restraints excluded: chain A residue 1161 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 60 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 108 optimal weight: 0.0270 chunk 116 optimal weight: 0.8980 chunk 96 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 GLN A 145 GLN ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 793 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9948 Z= 0.205 Angle : 0.767 15.561 13543 Z= 0.360 Chirality : 0.047 0.280 1576 Planarity : 0.005 0.046 1698 Dihedral : 16.380 177.270 1803 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.06 % Favored : 93.69 % Rotamer: Outliers : 2.41 % Allowed : 13.61 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.24), residues: 1194 helix: 0.44 (0.20), residues: 638 sheet: -1.26 (0.55), residues: 88 loop : -2.16 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 273 HIS 0.007 0.001 HIS A1042 PHE 0.026 0.001 PHE A 345 TYR 0.017 0.002 TYR A 570 ARG 0.005 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 102 time to evaluate : 0.918 Fit side-chains revert: symmetry clash REVERT: A 92 GLN cc_start: 0.6793 (OUTLIER) cc_final: 0.6392 (tt0) REVERT: A 260 TRP cc_start: 0.5733 (m-10) cc_final: 0.5169 (m-90) REVERT: A 586 GLU cc_start: 0.6857 (tp30) cc_final: 0.6542 (tp30) REVERT: A 666 SER cc_start: 0.8905 (OUTLIER) cc_final: 0.8474 (p) REVERT: A 932 TYR cc_start: 0.7637 (t80) cc_final: 0.7429 (t80) REVERT: A 1039 MET cc_start: 0.8464 (tmm) cc_final: 0.8230 (ttt) REVERT: A 1111 LEU cc_start: 0.8285 (tm) cc_final: 0.7748 (mt) outliers start: 24 outliers final: 8 residues processed: 116 average time/residue: 1.0384 time to fit residues: 130.9128 Evaluate side-chains 100 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 90 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 1043 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 11 optimal weight: 8.9990 chunk 51 optimal weight: 0.3980 chunk 72 optimal weight: 0.5980 chunk 108 optimal weight: 0.0870 chunk 115 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 145 GLN ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 793 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9948 Z= 0.190 Angle : 0.746 13.597 13543 Z= 0.347 Chirality : 0.046 0.276 1576 Planarity : 0.004 0.047 1698 Dihedral : 15.144 179.104 1799 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.57 % Favored : 93.18 % Rotamer: Outliers : 2.70 % Allowed : 15.25 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.24), residues: 1194 helix: 0.77 (0.21), residues: 638 sheet: -1.01 (0.56), residues: 88 loop : -1.83 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 273 HIS 0.007 0.001 HIS A1042 PHE 0.014 0.001 PHE A 209 TYR 0.016 0.001 TYR A 570 ARG 0.004 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 96 time to evaluate : 0.995 Fit side-chains revert: symmetry clash REVERT: A 192 TYR cc_start: 0.7422 (t80) cc_final: 0.7097 (t80) REVERT: A 241 GLN cc_start: 0.6943 (tt0) cc_final: 0.6435 (tm-30) REVERT: A 260 TRP cc_start: 0.5625 (m-10) cc_final: 0.5110 (m-90) REVERT: A 586 GLU cc_start: 0.6851 (tp30) cc_final: 0.6539 (tp30) REVERT: A 666 SER cc_start: 0.9085 (OUTLIER) cc_final: 0.8654 (p) REVERT: A 932 TYR cc_start: 0.7660 (t80) cc_final: 0.7441 (t80) outliers start: 27 outliers final: 12 residues processed: 114 average time/residue: 1.0794 time to fit residues: 133.4522 Evaluate side-chains 108 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 95 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1069 MET Chi-restraints excluded: chain A residue 1105 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 65 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 chunk 47 optimal weight: 6.9990 chunk 98 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 58 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 GLN A 145 GLN ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 530 HIS ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 793 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9948 Z= 0.219 Angle : 0.734 12.428 13543 Z= 0.344 Chirality : 0.046 0.288 1576 Planarity : 0.004 0.048 1698 Dihedral : 13.986 178.323 1796 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.31 % Favored : 93.43 % Rotamer: Outliers : 2.70 % Allowed : 15.73 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.25), residues: 1194 helix: 0.96 (0.21), residues: 639 sheet: -0.75 (0.58), residues: 88 loop : -1.61 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 949 HIS 0.006 0.001 HIS A1042 PHE 0.023 0.001 PHE A 360 TYR 0.017 0.001 TYR A1037 ARG 0.004 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 101 time to evaluate : 1.130 Fit side-chains revert: symmetry clash REVERT: A 192 TYR cc_start: 0.7576 (t80) cc_final: 0.7242 (t80) REVERT: A 206 THR cc_start: 0.8864 (OUTLIER) cc_final: 0.8652 (t) REVERT: A 260 TRP cc_start: 0.5525 (m-10) cc_final: 0.5013 (m-90) REVERT: A 586 GLU cc_start: 0.6874 (tp30) cc_final: 0.6558 (tp30) REVERT: A 666 SER cc_start: 0.9106 (OUTLIER) cc_final: 0.8665 (p) REVERT: A 748 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7953 (mt) REVERT: A 932 TYR cc_start: 0.7684 (t80) cc_final: 0.7464 (t80) outliers start: 27 outliers final: 15 residues processed: 114 average time/residue: 1.0932 time to fit residues: 136.2188 Evaluate side-chains 110 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 92 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1069 MET Chi-restraints excluded: chain A residue 1105 SER Chi-restraints excluded: chain A residue 1142 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 103 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 115 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 111 optimal weight: 0.6980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 793 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9948 Z= 0.328 Angle : 0.764 11.343 13543 Z= 0.368 Chirality : 0.049 0.313 1576 Planarity : 0.005 0.050 1698 Dihedral : 13.514 176.841 1796 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.90 % Favored : 92.85 % Rotamer: Outliers : 2.61 % Allowed : 16.12 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.25), residues: 1194 helix: 0.89 (0.20), residues: 637 sheet: -0.69 (0.59), residues: 88 loop : -1.56 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 949 HIS 0.005 0.001 HIS A1042 PHE 0.015 0.002 PHE A1167 TYR 0.022 0.002 TYR A1037 ARG 0.005 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 92 time to evaluate : 0.922 Fit side-chains revert: symmetry clash REVERT: A 192 TYR cc_start: 0.7618 (t80) cc_final: 0.7262 (t80) REVERT: A 206 THR cc_start: 0.8865 (OUTLIER) cc_final: 0.8652 (t) REVERT: A 260 TRP cc_start: 0.5667 (m-10) cc_final: 0.5158 (m-90) REVERT: A 586 GLU cc_start: 0.6900 (tp30) cc_final: 0.6574 (tp30) REVERT: A 666 SER cc_start: 0.9139 (OUTLIER) cc_final: 0.8686 (p) REVERT: A 748 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8040 (mt) outliers start: 26 outliers final: 20 residues processed: 105 average time/residue: 1.0131 time to fit residues: 115.9953 Evaluate side-chains 114 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 91 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1069 MET Chi-restraints excluded: chain A residue 1105 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 12 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 114 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 52 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 45 optimal weight: 0.1980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 GLN ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 793 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9948 Z= 0.186 Angle : 0.703 10.512 13543 Z= 0.334 Chirality : 0.045 0.281 1576 Planarity : 0.004 0.049 1698 Dihedral : 12.778 179.479 1796 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.14 % Favored : 93.60 % Rotamer: Outliers : 2.12 % Allowed : 16.99 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.25), residues: 1194 helix: 1.13 (0.21), residues: 637 sheet: -0.06 (0.63), residues: 78 loop : -1.53 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 949 HIS 0.005 0.001 HIS A1042 PHE 0.018 0.001 PHE A 360 TYR 0.017 0.001 TYR A 571 ARG 0.008 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 99 time to evaluate : 1.185 Fit side-chains revert: symmetry clash REVERT: A 192 TYR cc_start: 0.7578 (t80) cc_final: 0.7238 (t80) REVERT: A 260 TRP cc_start: 0.5426 (m-10) cc_final: 0.4935 (m-90) REVERT: A 586 GLU cc_start: 0.6892 (tp30) cc_final: 0.6582 (tp30) REVERT: A 666 SER cc_start: 0.9110 (OUTLIER) cc_final: 0.8675 (p) REVERT: A 748 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.8002 (mt) REVERT: A 857 ASP cc_start: 0.7227 (m-30) cc_final: 0.7019 (t70) REVERT: A 987 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8298 (mptt) REVERT: A 1234 LEU cc_start: 0.7858 (tt) cc_final: 0.7633 (tp) outliers start: 21 outliers final: 14 residues processed: 111 average time/residue: 0.9640 time to fit residues: 117.2970 Evaluate side-chains 107 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 90 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 987 LYS Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1069 MET Chi-restraints excluded: chain A residue 1105 SER Chi-restraints excluded: chain A residue 1142 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 68 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 0.0010 chunk 72 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 chunk 56 optimal weight: 6.9990 chunk 10 optimal weight: 30.0000 chunk 90 optimal weight: 3.9990 chunk 104 optimal weight: 0.6980 chunk 109 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 overall best weight: 0.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 GLN ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 793 ASN A 823 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9948 Z= 0.215 Angle : 0.710 9.813 13543 Z= 0.339 Chirality : 0.046 0.287 1576 Planarity : 0.004 0.049 1698 Dihedral : 12.488 178.733 1796 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.57 % Favored : 93.18 % Rotamer: Outliers : 2.51 % Allowed : 17.08 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.25), residues: 1194 helix: 1.20 (0.21), residues: 637 sheet: -0.03 (0.63), residues: 78 loop : -1.49 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 949 HIS 0.005 0.001 HIS A1042 PHE 0.016 0.001 PHE A 360 TYR 0.016 0.001 TYR A 571 ARG 0.007 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 93 time to evaluate : 0.924 Fit side-chains revert: symmetry clash REVERT: A 192 TYR cc_start: 0.7579 (t80) cc_final: 0.7234 (t80) REVERT: A 260 TRP cc_start: 0.5421 (m-10) cc_final: 0.4933 (m-90) REVERT: A 586 GLU cc_start: 0.6897 (tp30) cc_final: 0.6584 (tp30) REVERT: A 666 SER cc_start: 0.9120 (OUTLIER) cc_final: 0.8686 (p) REVERT: A 748 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.8040 (mt) REVERT: A 857 ASP cc_start: 0.7221 (m-30) cc_final: 0.7012 (t70) REVERT: A 987 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8309 (mptt) REVERT: A 1234 LEU cc_start: 0.7875 (tt) cc_final: 0.7656 (tp) outliers start: 25 outliers final: 16 residues processed: 106 average time/residue: 0.9978 time to fit residues: 115.4768 Evaluate side-chains 110 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 91 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 987 LYS Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1069 MET Chi-restraints excluded: chain A residue 1105 SER Chi-restraints excluded: chain A residue 1142 MET Chi-restraints excluded: chain A residue 1161 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 83 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN A 200 GLN ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 793 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9948 Z= 0.196 Angle : 0.696 10.640 13543 Z= 0.330 Chirality : 0.045 0.280 1576 Planarity : 0.004 0.049 1698 Dihedral : 11.876 179.206 1796 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.40 % Favored : 93.35 % Rotamer: Outliers : 2.22 % Allowed : 17.47 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.25), residues: 1194 helix: 1.34 (0.21), residues: 637 sheet: -0.14 (0.63), residues: 80 loop : -1.48 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 949 HIS 0.005 0.001 HIS A1042 PHE 0.017 0.001 PHE A 360 TYR 0.016 0.001 TYR A 571 ARG 0.006 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 95 time to evaluate : 0.932 Fit side-chains revert: symmetry clash REVERT: A 192 TYR cc_start: 0.7537 (t80) cc_final: 0.7139 (t80) REVERT: A 260 TRP cc_start: 0.5343 (m-10) cc_final: 0.4879 (m-90) REVERT: A 586 GLU cc_start: 0.6902 (tp30) cc_final: 0.6591 (tp30) REVERT: A 666 SER cc_start: 0.9115 (OUTLIER) cc_final: 0.8684 (p) REVERT: A 748 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.8030 (mt) outliers start: 22 outliers final: 15 residues processed: 106 average time/residue: 1.0551 time to fit residues: 122.2442 Evaluate side-chains 113 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 96 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1069 MET Chi-restraints excluded: chain A residue 1105 SER Chi-restraints excluded: chain A residue 1142 MET Chi-restraints excluded: chain A residue 1161 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 53 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 72 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 74 optimal weight: 0.0170 chunk 100 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.9022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 793 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9948 Z= 0.215 Angle : 0.705 11.266 13543 Z= 0.337 Chirality : 0.045 0.286 1576 Planarity : 0.004 0.050 1698 Dihedral : 11.522 178.646 1796 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.90 % Favored : 92.85 % Rotamer: Outliers : 1.83 % Allowed : 18.15 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.25), residues: 1194 helix: 1.34 (0.21), residues: 637 sheet: -0.11 (0.63), residues: 80 loop : -1.50 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 949 HIS 0.005 0.001 HIS A1042 PHE 0.016 0.001 PHE A 360 TYR 0.017 0.001 TYR A1037 ARG 0.006 0.000 ARG A 161 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 98 time to evaluate : 1.014 Fit side-chains revert: symmetry clash REVERT: A 192 TYR cc_start: 0.7539 (t80) cc_final: 0.7153 (t80) REVERT: A 260 TRP cc_start: 0.5289 (m-10) cc_final: 0.4822 (m-90) REVERT: A 586 GLU cc_start: 0.6911 (tp30) cc_final: 0.6591 (tp30) REVERT: A 666 SER cc_start: 0.9118 (OUTLIER) cc_final: 0.8683 (p) REVERT: A 748 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.8053 (mt) REVERT: A 987 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8376 (mptt) outliers start: 18 outliers final: 15 residues processed: 109 average time/residue: 1.0184 time to fit residues: 121.2750 Evaluate side-chains 112 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 94 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 987 LYS Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1069 MET Chi-restraints excluded: chain A residue 1105 SER Chi-restraints excluded: chain A residue 1142 MET Chi-restraints excluded: chain A residue 1161 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 87 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 26 optimal weight: 0.0070 chunk 94 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 97 optimal weight: 0.9990 chunk 11 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 83 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 793 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.160994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.120407 restraints weight = 31337.849| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 6.32 r_work: 0.2821 rms_B_bonded: 5.52 restraints_weight: 2.0000 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2786 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2786 r_free = 0.2786 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2786 r_free = 0.2786 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2786 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9948 Z= 0.189 Angle : 0.683 9.799 13543 Z= 0.327 Chirality : 0.044 0.279 1576 Planarity : 0.004 0.049 1698 Dihedral : 11.080 179.682 1796 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.40 % Favored : 93.35 % Rotamer: Outliers : 1.83 % Allowed : 18.34 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.25), residues: 1194 helix: 1.43 (0.21), residues: 637 sheet: -0.15 (0.57), residues: 92 loop : -1.50 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 273 HIS 0.005 0.001 HIS A1042 PHE 0.025 0.001 PHE A 345 TYR 0.016 0.001 TYR A 571 ARG 0.006 0.000 ARG A 161 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3124.21 seconds wall clock time: 60 minutes 1.87 seconds (3601.87 seconds total)