Starting phenix.real_space_refine on Mon Nov 18 21:08:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9avg_43901/11_2024/9avg_43901.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9avg_43901/11_2024/9avg_43901.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9avg_43901/11_2024/9avg_43901.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9avg_43901/11_2024/9avg_43901.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9avg_43901/11_2024/9avg_43901.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9avg_43901/11_2024/9avg_43901.cif" } resolution = 3.6 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= 0.002 sd= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 6 9.91 5 P 3 5.49 5 S 93 5.16 5 Cl 2 4.86 5 C 11311 2.51 5 N 2883 2.21 5 O 3200 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 17498 Number of models: 1 Model: "" Number of chains: 13 Chain: "Q" Number of atoms: 6280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 797, 6280 Classifications: {'peptide': 797} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'CIS': 1, 'PTRANS': 31, 'TRANS': 764} Chain breaks: 3 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 49 Chain: "R" Number of atoms: 6294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 796, 6294 Classifications: {'peptide': 796} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'CIS': 1, 'PTRANS': 31, 'TRANS': 763} Chain breaks: 3 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 43 Chain: "A" Number of atoms: 1738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1738 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 6, 'TRANS': 216} Chain breaks: 2 Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 87 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 4, 'ASN:plan1': 3, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 81 Chain: "B" Number of atoms: 2450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2450 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 116 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 91 Chain: "G" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 22 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" 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: "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: "F" 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: "Q" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 58 Unusual residues: {'NAG': 3, 'TCR': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 64 Unusual residues: {' CA': 3, '9IG': 1, 'PO4': 1, 'Y01': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "R" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 44 Unusual residues: {'NAG': 2, 'TCR': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 80 Unusual residues: {' CA': 3, '9IG': 1, 'A1AF7': 1, 'PO4': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 9.29, per 1000 atoms: 0.53 Number of scatterers: 17498 At special positions: 0 Unit cell: (117.15, 97.35, 237.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 6 19.99 Cl 2 17.00 S 93 16.00 P 3 15.00 O 3200 8.00 N 2883 7.00 C 11311 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS Q 60 " - pdb=" SG CYS Q 101 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 236 " - pdb=" SG CYS Q 561 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 358 " - pdb=" SG CYS Q 395 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 437 " - pdb=" SG CYS Q 449 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 542 " - pdb=" SG CYS Q 562 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 546 " - pdb=" SG CYS Q 565 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 677 " - pdb=" SG CYS Q 765 " distance=2.03 Simple disulfide: pdb=" SG CYS R 60 " - pdb=" SG CYS R 101 " distance=2.03 Simple disulfide: pdb=" SG CYS R 236 " - pdb=" SG CYS R 561 " distance=2.03 Simple disulfide: pdb=" SG CYS R 358 " - pdb=" SG CYS R 395 " distance=2.03 Simple disulfide: pdb=" SG CYS R 437 " - pdb=" SG CYS R 449 " distance=2.03 Simple disulfide: pdb=" SG CYS R 542 " - pdb=" SG CYS R 562 " distance=2.03 Simple disulfide: pdb=" SG CYS R 546 " - pdb=" SG CYS R 565 " distance=2.03 Simple disulfide: pdb=" SG CYS R 568 " - pdb=" SG CYS R 582 " distance=2.03 Simple disulfide: pdb=" SG CYS R 585 " - pdb=" SG CYS R 598 " distance=2.03 Simple disulfide: pdb=" SG CYS R 677 " - pdb=" SG CYS R 765 " 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 BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG C 1 " - " ASN Q 488 " " NAG D 1 " - " ASN Q 541 " " NAG E 1 " - " ASN R 488 " " NAG F 1 " - " ASN R 541 " " NAG Q1001 " - " ASN Q 261 " " NAG Q1002 " - " ASN Q 287 " " NAG Q1003 " - " ASN Q 468 " " NAG R1001 " - " ASN R 287 " " NAG R1002 " - " ASN R 468 " Time building additional restraints: 5.08 Conformation dependent library (CDL) restraints added in 2.4 seconds 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4164 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 24 sheets defined 45.4% alpha, 15.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.41 Creating SS restraints... Processing helix chain 'Q' and resid 64 through 83 Processing helix chain 'Q' and resid 103 through 113 Processing helix chain 'Q' and resid 115 through 123 Processing helix chain 'Q' and resid 146 through 158 Processing helix chain 'Q' and resid 171 through 176 removed outlier: 3.609A pdb=" N LEU Q 174 " --> pdb=" O SER Q 171 " (cutoff:3.500A) Processing helix chain 'Q' and resid 190 through 204 Processing helix chain 'Q' and resid 218 through 233 removed outlier: 3.551A pdb=" N GLY Q 222 " --> pdb=" O TYR Q 218 " (cutoff:3.500A) Processing helix chain 'Q' and resid 248 through 261 Processing helix chain 'Q' and resid 272 through 287 Proline residue: Q 278 - end of helix Processing helix chain 'Q' and resid 307 through 309 No H-bonds generated for 'chain 'Q' and resid 307 through 309' Processing helix chain 'Q' and resid 310 through 315 Processing helix chain 'Q' and resid 329 through 336 Processing helix chain 'Q' and resid 347 through 357 Processing helix chain 'Q' and resid 415 through 436 Processing helix chain 'Q' and resid 438 through 442 removed outlier: 3.866A pdb=" N GLY Q 442 " --> pdb=" O PRO Q 439 " (cutoff:3.500A) Processing helix chain 'Q' and resid 444 through 448 Processing helix chain 'Q' and resid 456 through 466 Processing helix chain 'Q' and resid 525 through 528 Processing helix chain 'Q' and resid 529 through 533 Processing helix chain 'Q' and resid 610 through 637 Processing helix chain 'Q' and resid 640 through 646 removed outlier: 3.755A pdb=" N THR Q 646 " --> pdb=" O ILE Q 642 " (cutoff:3.500A) Processing helix chain 'Q' and resid 647 through 665 removed outlier: 3.729A pdb=" N SER Q 665 " --> pdb=" O CYS Q 661 " (cutoff:3.500A) Processing helix chain 'Q' and resid 666 through 669 Processing helix chain 'Q' and resid 673 through 699 removed outlier: 4.976A pdb=" N GLN Q 681 " --> pdb=" O CYS Q 677 " (cutoff:3.500A) Proline residue: Q 682 - end of helix Processing helix chain 'Q' and resid 702 through 708 Processing helix chain 'Q' and resid 723 through 746 removed outlier: 4.092A pdb=" N GLN Q 735 " --> pdb=" O CYS Q 731 " (cutoff:3.500A) Processing helix chain 'Q' and resid 769 through 793 removed outlier: 3.721A pdb=" N LYS Q 793 " --> pdb=" O PHE Q 789 " (cutoff:3.500A) Processing helix chain 'Q' and resid 802 through 820 Processing helix chain 'Q' and resid 820 through 827 removed outlier: 3.690A pdb=" N ALA Q 824 " --> pdb=" O SER Q 820 " (cutoff:3.500A) Processing helix chain 'Q' and resid 831 through 862 removed outlier: 4.093A pdb=" N ALA Q 835 " --> pdb=" O LYS Q 831 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ASN Q 855 " --> pdb=" O CYS Q 851 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N LYS Q 856 " --> pdb=" O ILE Q 852 " (cutoff:3.500A) Processing helix chain 'Q' and resid 863 through 867 removed outlier: 3.663A pdb=" N ARG Q 866 " --> pdb=" O LYS Q 863 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 84 Processing helix chain 'R' and resid 103 through 115 Processing helix chain 'R' and resid 115 through 122 Processing helix chain 'R' and resid 146 through 158 removed outlier: 3.641A pdb=" N LEU R 156 " --> pdb=" O ALA R 152 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 176 Processing helix chain 'R' and resid 190 through 204 Processing helix chain 'R' and resid 218 through 233 removed outlier: 3.503A pdb=" N GLY R 222 " --> pdb=" O TYR R 218 " (cutoff:3.500A) Processing helix chain 'R' and resid 248 through 261 Processing helix chain 'R' and resid 272 through 286 Proline residue: R 278 - end of helix Processing helix chain 'R' and resid 296 through 301 removed outlier: 4.413A pdb=" N SER R 301 " --> pdb=" O GLU R 297 " (cutoff:3.500A) Processing helix chain 'R' and resid 307 through 309 No H-bonds generated for 'chain 'R' and resid 307 through 309' Processing helix chain 'R' and resid 310 through 315 Processing helix chain 'R' and resid 329 through 336 Processing helix chain 'R' and resid 347 through 357 Processing helix chain 'R' and resid 400 through 404 Processing helix chain 'R' and resid 415 through 436 Processing helix chain 'R' and resid 444 through 448 Processing helix chain 'R' and resid 451 through 455 removed outlier: 3.843A pdb=" N VAL R 455 " --> pdb=" O ILE R 452 " (cutoff:3.500A) Processing helix chain 'R' and resid 456 through 465 Processing helix chain 'R' and resid 525 through 528 Processing helix chain 'R' and resid 529 through 533 Processing helix chain 'R' and resid 610 through 637 Processing helix chain 'R' and resid 640 through 645 Processing helix chain 'R' and resid 647 through 665 removed outlier: 3.630A pdb=" N SER R 665 " --> pdb=" O CYS R 661 " (cutoff:3.500A) Processing helix chain 'R' and resid 666 through 669 Processing helix chain 'R' and resid 673 through 708 removed outlier: 4.752A pdb=" N GLN R 681 " --> pdb=" O CYS R 677 " (cutoff:3.500A) Proline residue: R 682 - end of helix Processing helix chain 'R' and resid 719 through 746 Processing helix chain 'R' and resid 770 through 794 removed outlier: 3.632A pdb=" N THR R 780 " --> pdb=" O LEU R 776 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA R 785 " --> pdb=" O CYS R 781 " (cutoff:3.500A) Processing helix chain 'R' and resid 798 through 802 Processing helix chain 'R' and resid 803 through 821 Processing helix chain 'R' and resid 821 through 827 removed outlier: 3.771A pdb=" N SER R 827 " --> pdb=" O PRO R 823 " (cutoff:3.500A) Processing helix chain 'R' and resid 830 through 861 removed outlier: 3.970A pdb=" N SER R 834 " --> pdb=" O GLY R 830 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ASN R 855 " --> pdb=" O CYS R 851 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N LYS R 856 " --> pdb=" O ILE R 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 7 through 31 removed outlier: 3.739A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 56 removed outlier: 4.163A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A 56 " --> pdb=" O GLN A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 130 removed outlier: 3.715A pdb=" N GLN A 119 " --> pdb=" O TYR A 115 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLU A 120 " --> pdb=" O ASN A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 155 removed outlier: 3.504A pdb=" N ALA A 155 " --> pdb=" O GLU A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 164 removed outlier: 4.365A pdb=" N TYR A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 168 Processing helix chain 'A' and resid 183 through 204 removed outlier: 4.154A pdb=" N ILE A 200 " --> pdb=" O GLU A 196 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER A 201 " --> pdb=" O PHE A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 243 Processing helix chain 'B' and resid 5 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 9 through 24 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.653A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Q' and resid 26 through 28 removed outlier: 6.054A pdb=" N ILE Q 32 " --> pdb=" O GLY Q 94 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N ARG Q 96 " --> pdb=" O ILE Q 32 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU Q 34 " --> pdb=" O ARG Q 96 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N PHE Q 98 " --> pdb=" O LEU Q 34 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N GLY Q 36 " --> pdb=" O PHE Q 98 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE Q 33 " --> pdb=" O THR Q 138 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ALA Q 140 " --> pdb=" O ILE Q 33 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N VAL Q 165 " --> pdb=" O ILE Q 139 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL Q 141 " --> pdb=" O VAL Q 165 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N GLN Q 164 " --> pdb=" O LEU Q 184 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'Q' and resid 41 through 44 removed outlier: 6.247A pdb=" N HIS Q 41 " --> pdb=" O TYR Q 63 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TYR Q 63 " --> pdb=" O HIS Q 41 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'Q' and resid 236 through 243 removed outlier: 7.954A pdb=" N VAL Q 209 " --> pdb=" O ASP Q 238 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N SER Q 240 " --> pdb=" O VAL Q 209 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N THR Q 211 " --> pdb=" O SER Q 240 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N LEU Q 242 " --> pdb=" O THR Q 211 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ALA Q 213 " --> pdb=" O LEU Q 242 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N TRP Q 208 " --> pdb=" O VAL Q 266 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N VAL Q 268 " --> pdb=" O TRP Q 208 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLY Q 210 " --> pdb=" O VAL Q 268 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N PHE Q 270 " --> pdb=" O GLY Q 210 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ILE Q 212 " --> pdb=" O PHE Q 270 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N TYR Q 489 " --> pdb=" O TYR Q 510 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N TYR Q 510 " --> pdb=" O TYR Q 489 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE Q 491 " --> pdb=" O VAL Q 508 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'Q' and resid 468 through 470 Processing sheet with id=AA5, first strand: chain 'Q' and resid 550 through 554 Processing sheet with id=AA6, first strand: chain 'Q' and resid 572 through 573 Processing sheet with id=AA7, first strand: chain 'Q' and resid 589 through 591 Processing sheet with id=AA8, first strand: chain 'Q' and resid 602 through 604 Processing sheet with id=AA9, first strand: chain 'R' and resid 25 through 28 removed outlier: 6.212A pdb=" N ILE R 32 " --> pdb=" O GLY R 94 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ARG R 96 " --> pdb=" O ILE R 32 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU R 34 " --> pdb=" O ARG R 96 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N PHE R 98 " --> pdb=" O LEU R 34 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N GLY R 36 " --> pdb=" O PHE R 98 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE R 33 " --> pdb=" O THR R 138 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA R 140 " --> pdb=" O ILE R 33 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N VAL R 165 " --> pdb=" O ILE R 139 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VAL R 141 " --> pdb=" O VAL R 165 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N GLN R 164 " --> pdb=" O LEU R 184 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 236 through 243 removed outlier: 6.556A pdb=" N VAL R 209 " --> pdb=" O ILE R 237 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N PHE R 239 " --> pdb=" O VAL R 209 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N VAL R 266 " --> pdb=" O TRP R 208 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ILE R 267 " --> pdb=" O LEU R 294 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N TRP R 293 " --> pdb=" O ILE R 318 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N PHE R 320 " --> pdb=" O TRP R 293 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ALA R 295 " --> pdb=" O PHE R 320 " (cutoff:3.500A) removed outlier: 9.422A pdb=" N LEU R 322 " --> pdb=" O ALA R 295 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N TYR R 489 " --> pdb=" O TYR R 510 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N TYR R 510 " --> pdb=" O TYR R 489 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE R 491 " --> pdb=" O VAL R 508 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 469 through 470 removed outlier: 3.525A pdb=" N PHE R 469 " --> pdb=" O VAL R 477 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'R' and resid 550 through 554 Processing sheet with id=AB4, first strand: chain 'R' and resid 572 through 573 Processing sheet with id=AB5, first strand: chain 'R' and resid 589 through 591 Processing sheet with id=AB6, first strand: chain 'R' and resid 602 through 604 removed outlier: 5.970A pdb=" N GLU R 602 " --> pdb=" O ILE R 761 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ILE R 763 " --> pdb=" O GLU R 602 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLU R 604 " --> pdb=" O ILE R 763 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N CYS R 765 " --> pdb=" O GLU R 604 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 75 through 76 removed outlier: 3.884A pdb=" N ALA A 105 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 37 " --> pdb=" O ALA A 105 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 109 through 111 removed outlier: 5.847A pdb=" N VAL A 110 " --> pdb=" O ASN A 144 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 46 through 52 removed outlier: 5.744A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.751A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.304A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 149 through 151 removed outlier: 3.934A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.929A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 229 through 232 removed outlier: 6.402A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.789A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 837 hydrogen bonds defined for protein. 2406 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.02 Time building geometry restraints manager: 5.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4666 1.33 - 1.45: 3780 1.45 - 1.58: 9345 1.58 - 1.70: 2 1.70 - 1.82: 114 Bond restraints: 17907 Sorted by residual: bond pdb=" CAI Y01 Q1010 " pdb=" CAK Y01 Q1010 " ideal model delta sigma weight residual 1.492 1.406 0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" CB TCR R1003 " pdb=" CG TCR R1003 " ideal model delta sigma weight residual 1.494 1.426 0.068 2.00e-02 2.50e+03 1.14e+01 bond pdb=" O3 PO4 R1004 " pdb=" P PO4 R1004 " ideal model delta sigma weight residual 1.569 1.504 0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" O2 PO4 R1004 " pdb=" P PO4 R1004 " ideal model delta sigma weight residual 1.567 1.503 0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" O3 PO4 Q1005 " pdb=" P PO4 Q1005 " ideal model delta sigma weight residual 1.569 1.505 0.064 2.00e-02 2.50e+03 1.01e+01 ... (remaining 17902 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 23964 2.35 - 4.69: 331 4.69 - 7.04: 25 7.04 - 9.39: 5 9.39 - 11.74: 3 Bond angle restraints: 24328 Sorted by residual: angle pdb=" C ALA A 7 " pdb=" CA ALA A 7 " pdb=" CB ALA A 7 " ideal model delta sigma weight residual 116.63 110.19 6.44 1.16e+00 7.43e-01 3.08e+01 angle pdb=" C LEU R 743 " pdb=" N TYR R 744 " pdb=" CA TYR R 744 " ideal model delta sigma weight residual 122.26 115.93 6.33 1.59e+00 3.96e-01 1.59e+01 angle pdb=" OAG Y01 Q1010 " pdb=" CAY Y01 Q1010 " pdb=" OAW Y01 Q1010 " ideal model delta sigma weight residual 123.38 111.64 11.74 3.00e+00 1.11e-01 1.53e+01 angle pdb=" CAM Y01 Q1010 " pdb=" CAY Y01 Q1010 " pdb=" OAW Y01 Q1010 " ideal model delta sigma weight residual 111.19 122.63 -11.44 3.00e+00 1.11e-01 1.45e+01 angle pdb=" N ILE A 193 " pdb=" CA ILE A 193 " pdb=" CB ILE A 193 " ideal model delta sigma weight residual 110.55 114.66 -4.11 1.17e+00 7.31e-01 1.23e+01 ... (remaining 24323 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.06: 9874 18.06 - 36.12: 742 36.12 - 54.18: 112 54.18 - 72.24: 30 72.24 - 90.29: 8 Dihedral angle restraints: 10766 sinusoidal: 4338 harmonic: 6428 Sorted by residual: dihedral pdb=" CA PHE A 142 " pdb=" C PHE A 142 " pdb=" N LEU A 143 " pdb=" CA LEU A 143 " ideal model delta harmonic sigma weight residual 180.00 157.42 22.58 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA ILE Q 852 " pdb=" C ILE Q 852 " pdb=" N PHE Q 853 " pdb=" CA PHE Q 853 " ideal model delta harmonic sigma weight residual -180.00 -159.07 -20.93 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 159.70 20.30 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 10763 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2138 0.048 - 0.097: 525 0.097 - 0.145: 117 0.145 - 0.194: 6 0.194 - 0.242: 4 Chirality restraints: 2790 Sorted by residual: chirality pdb=" C02 A1AF7 R1009 " pdb=" C01 A1AF7 R1009 " pdb=" C03 A1AF7 R1009 " pdb=" O01 A1AF7 R1009 " both_signs ideal model delta sigma weight residual False 2.54 2.78 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" C1 NAG Q1002 " pdb=" ND2 ASN Q 287 " pdb=" C2 NAG Q1002 " pdb=" O5 NAG Q1002 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CB ILE B 81 " pdb=" CA ILE B 81 " pdb=" CG1 ILE B 81 " pdb=" CG2 ILE B 81 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 2787 not shown) Planarity restraints: 3065 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG R 54 " -0.055 5.00e-02 4.00e+02 8.25e-02 1.09e+01 pdb=" N PRO R 55 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO R 55 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO R 55 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS Q 568 " 0.041 5.00e-02 4.00e+02 6.21e-02 6.17e+00 pdb=" N PRO Q 569 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO Q 569 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO Q 569 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA Q 850 " -0.012 2.00e-02 2.50e+03 2.44e-02 5.95e+00 pdb=" C ALA Q 850 " 0.042 2.00e-02 2.50e+03 pdb=" O ALA Q 850 " -0.016 2.00e-02 2.50e+03 pdb=" N CYS Q 851 " -0.014 2.00e-02 2.50e+03 ... (remaining 3062 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 280 2.67 - 3.23: 17178 3.23 - 3.78: 28491 3.78 - 4.34: 39608 4.34 - 4.90: 63001 Nonbonded interactions: 148558 Sorted by model distance: nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.112 3.040 nonbonded pdb=" O MET A 18 " pdb=" NE2 GLN A 22 " model vdw 2.207 3.120 nonbonded pdb=" NE2 HIS B 54 " pdb=" OG SER B 72 " model vdw 2.218 3.120 nonbonded pdb=" OD2 ASP R 238 " pdb=" OG SER R 262 " model vdw 2.226 3.040 nonbonded pdb=" OG1 THR R 470 " pdb=" OE1 GLN R 476 " model vdw 2.226 3.040 ... (remaining 148553 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 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = (chain 'Q' and (resid 22 through 49 or (resid 50 and (name N or name CA or name \ C or name O or name CB )) or resid 51 through 120 or (resid 121 and (name N or n \ ame CA or name C or name O or name CB )) or resid 122 or resid 135 through 230 o \ r (resid 231 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 32 through 360 or (resid 392 and (name N or name CA or name C or name O or name \ CB )) or resid 393 through 404 or (resid 405 and (name N or name CA or name C or \ name O or name CB )) or resid 406 through 518 or (resid 519 and (name N or name \ CA or name C or name O or name CB )) or resid 520 through 864 or resid 1002 thr \ ough 1004 or resid 1005 through 1009)) selection = (chain 'R' and (resid 22 through 46 or (resid 47 through 48 and (name N or name \ CA or name C or name O or name CB )) or resid 49 through 55 or (resid 56 and (na \ me N or name CA or name C or name O or name CB )) or resid 57 through 247 or (re \ sid 248 through 250 and (name N or name CA or name C or name O or name CB )) or \ resid 251 through 453 or (resid 454 and (name N or name CA or name C or name O o \ r name CB )) or resid 455 through 499 or (resid 500 and (name N or name CA or na \ me C or name O or name CB )) or resid 501 through 525 or (resid 526 and (name N \ or name CA or name C or name O or name CB )) or resid 527 through 609 or (resid \ 610 and (name N or name CA or name C or name O or name CB )) or resid 611 throug \ h 637 or (resid 638 and (name N or name CA or name C or name O or name CB )) or \ resid 639 through 708 or resid 722 through 864 or resid 1001 through 1003 or res \ id 1004 through 1008)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 19.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 5.090 Set scattering table: 0.000 Process input model: 39.360 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 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 0.086 17907 Z= 0.327 Angle : 0.692 11.736 24328 Z= 0.381 Chirality : 0.044 0.242 2790 Planarity : 0.005 0.082 3056 Dihedral : 12.938 90.294 6554 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.17), residues: 2182 helix: 0.25 (0.16), residues: 911 sheet: -1.52 (0.26), residues: 371 loop : -0.80 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP R 352 HIS 0.008 0.001 HIS A 209 PHE 0.033 0.002 PHE Q 634 TYR 0.014 0.002 TYR B 289 ARG 0.007 0.001 ARG R 25 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 384 time to evaluate : 2.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 92 THR cc_start: 0.6822 (t) cc_final: 0.6593 (t) REVERT: R 248 ASP cc_start: 0.6710 (m-30) cc_final: 0.6418 (m-30) REVERT: R 309 GLN cc_start: 0.8048 (pm20) cc_final: 0.7666 (pm20) REVERT: A 38 LEU cc_start: 0.8231 (tp) cc_final: 0.8013 (tp) REVERT: A 122 LEU cc_start: 0.7931 (tp) cc_final: 0.7643 (tp) REVERT: A 235 ILE cc_start: 0.8711 (mm) cc_final: 0.8403 (mp) REVERT: B 36 ASN cc_start: 0.5165 (m-40) cc_final: 0.4784 (p0) REVERT: B 81 ILE cc_start: 0.8370 (tp) cc_final: 0.8158 (tp) REVERT: B 333 ASP cc_start: 0.7677 (p0) cc_final: 0.6411 (t0) outliers start: 0 outliers final: 0 residues processed: 384 average time/residue: 0.3395 time to fit residues: 196.9703 Evaluate side-chains 348 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 348 time to evaluate : 1.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 184 optimal weight: 0.8980 chunk 165 optimal weight: 0.0870 chunk 91 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 111 optimal weight: 0.9990 chunk 88 optimal weight: 0.1980 chunk 170 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 103 optimal weight: 0.5980 chunk 127 optimal weight: 0.9990 chunk 197 optimal weight: 0.7980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.0906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17907 Z= 0.257 Angle : 0.555 7.651 24328 Z= 0.297 Chirality : 0.043 0.167 2790 Planarity : 0.005 0.062 3056 Dihedral : 7.589 65.123 2791 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.89 % Allowed : 6.77 % Favored : 92.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.17), residues: 2182 helix: 0.66 (0.16), residues: 919 sheet: -1.48 (0.26), residues: 373 loop : -0.73 (0.20), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 297 HIS 0.008 0.001 HIS A 209 PHE 0.022 0.002 PHE R 788 TYR 0.013 0.002 TYR R 421 ARG 0.005 0.000 ARG Q 62 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 372 time to evaluate : 1.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 248 ASP cc_start: 0.6570 (m-30) cc_final: 0.6131 (m-30) REVERT: R 282 GLU cc_start: 0.6643 (tp30) cc_final: 0.6429 (tp30) REVERT: R 309 GLN cc_start: 0.8098 (pm20) cc_final: 0.7510 (pm20) REVERT: A 38 LEU cc_start: 0.8201 (tp) cc_final: 0.7975 (tp) REVERT: A 122 LEU cc_start: 0.7879 (tp) cc_final: 0.7619 (tp) REVERT: A 186 VAL cc_start: 0.6591 (t) cc_final: 0.6341 (t) REVERT: A 192 PHE cc_start: 0.6621 (t80) cc_final: 0.6390 (t80) REVERT: A 234 ILE cc_start: 0.8965 (OUTLIER) cc_final: 0.8683 (mp) REVERT: A 235 ILE cc_start: 0.8729 (mm) cc_final: 0.8403 (mp) REVERT: B 198 LEU cc_start: 0.8975 (mm) cc_final: 0.8679 (mp) REVERT: B 263 THR cc_start: 0.7098 (m) cc_final: 0.6645 (p) REVERT: B 311 HIS cc_start: 0.6509 (m-70) cc_final: 0.6301 (m-70) outliers start: 16 outliers final: 12 residues processed: 377 average time/residue: 0.3211 time to fit residues: 181.6826 Evaluate side-chains 358 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 345 time to evaluate : 2.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 485 LEU Chi-restraints excluded: chain Q residue 566 VAL Chi-restraints excluded: chain Q residue 727 LEU Chi-restraints excluded: chain Q residue 736 ILE Chi-restraints excluded: chain Q residue 740 VAL Chi-restraints excluded: chain R residue 336 LYS Chi-restraints excluded: chain R residue 592 ASN Chi-restraints excluded: chain R residue 609 THR Chi-restraints excluded: chain R residue 624 ILE Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 110 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 164 optimal weight: 3.9990 chunk 134 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 198 optimal weight: 3.9990 chunk 214 optimal weight: 0.9980 chunk 176 optimal weight: 4.9990 chunk 196 optimal weight: 1.9990 chunk 67 optimal weight: 0.0170 chunk 159 optimal weight: 0.8980 overall best weight: 0.7818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 17907 Z= 0.360 Angle : 0.576 7.770 24328 Z= 0.307 Chirality : 0.045 0.213 2790 Planarity : 0.005 0.051 3056 Dihedral : 7.392 69.569 2791 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.89 % Allowed : 9.77 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.17), residues: 2182 helix: 0.64 (0.16), residues: 920 sheet: -1.42 (0.26), residues: 366 loop : -0.72 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.006 0.001 HIS Q 338 PHE 0.026 0.002 PHE R 788 TYR 0.020 0.002 TYR R 744 ARG 0.007 0.001 ARG Q 185 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 362 time to evaluate : 2.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 702 VAL cc_start: 0.7082 (OUTLIER) cc_final: 0.6755 (t) REVERT: R 248 ASP cc_start: 0.6525 (m-30) cc_final: 0.6163 (m-30) REVERT: R 422 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7515 (mp) REVERT: A 106 ILE cc_start: 0.8266 (mm) cc_final: 0.8006 (mm) REVERT: A 122 LEU cc_start: 0.7901 (tp) cc_final: 0.7616 (tp) REVERT: A 186 VAL cc_start: 0.6579 (t) cc_final: 0.6338 (t) REVERT: A 192 PHE cc_start: 0.6692 (t80) cc_final: 0.6428 (t80) REVERT: A 234 ILE cc_start: 0.8951 (OUTLIER) cc_final: 0.8688 (mp) REVERT: B 36 ASN cc_start: 0.5198 (m-40) cc_final: 0.4813 (p0) REVERT: B 81 ILE cc_start: 0.8533 (tp) cc_final: 0.8231 (tp) REVERT: B 198 LEU cc_start: 0.8984 (mm) cc_final: 0.8713 (mp) REVERT: B 263 THR cc_start: 0.7131 (m) cc_final: 0.6659 (p) outliers start: 34 outliers final: 22 residues processed: 376 average time/residue: 0.3325 time to fit residues: 185.7625 Evaluate side-chains 373 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 348 time to evaluate : 1.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 92 THR Chi-restraints excluded: chain Q residue 409 ILE Chi-restraints excluded: chain Q residue 422 LEU Chi-restraints excluded: chain Q residue 436 THR Chi-restraints excluded: chain Q residue 485 LEU Chi-restraints excluded: chain Q residue 566 VAL Chi-restraints excluded: chain Q residue 702 VAL Chi-restraints excluded: chain Q residue 727 LEU Chi-restraints excluded: chain Q residue 736 ILE Chi-restraints excluded: chain Q residue 740 VAL Chi-restraints excluded: chain Q residue 860 ILE Chi-restraints excluded: chain R residue 422 LEU Chi-restraints excluded: chain R residue 592 ASN Chi-restraints excluded: chain R residue 609 THR Chi-restraints excluded: chain R residue 624 ILE Chi-restraints excluded: chain R residue 739 CYS Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 195 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 133 optimal weight: 0.9990 chunk 199 optimal weight: 0.5980 chunk 210 optimal weight: 5.9990 chunk 103 optimal weight: 0.6980 chunk 188 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 17907 Z= 0.377 Angle : 0.579 7.757 24328 Z= 0.307 Chirality : 0.045 0.145 2790 Planarity : 0.004 0.054 3056 Dihedral : 7.288 72.618 2791 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.77 % Allowed : 11.27 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.17), residues: 2182 helix: 0.59 (0.16), residues: 923 sheet: -1.44 (0.26), residues: 366 loop : -0.78 (0.20), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP Q 299 HIS 0.005 0.001 HIS A 209 PHE 0.023 0.002 PHE A 100 TYR 0.022 0.002 TYR R 744 ARG 0.006 0.001 ARG Q 185 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 360 time to evaluate : 1.980 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 422 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7578 (mt) REVERT: Q 702 VAL cc_start: 0.7090 (OUTLIER) cc_final: 0.6758 (t) REVERT: R 248 ASP cc_start: 0.6518 (m-30) cc_final: 0.6128 (m-30) REVERT: R 282 GLU cc_start: 0.6672 (tp30) cc_final: 0.6448 (tp30) REVERT: R 422 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7537 (mp) REVERT: A 106 ILE cc_start: 0.8303 (mm) cc_final: 0.7998 (mm) REVERT: A 122 LEU cc_start: 0.7907 (tp) cc_final: 0.7624 (tp) REVERT: A 186 VAL cc_start: 0.6749 (t) cc_final: 0.6519 (t) REVERT: A 192 PHE cc_start: 0.6627 (t80) cc_final: 0.6341 (t80) REVERT: A 234 ILE cc_start: 0.8931 (OUTLIER) cc_final: 0.8656 (mp) REVERT: A 235 ILE cc_start: 0.8714 (mm) cc_final: 0.8461 (mp) REVERT: B 36 ASN cc_start: 0.5179 (m-40) cc_final: 0.4812 (p0) REVERT: B 198 LEU cc_start: 0.8981 (mm) cc_final: 0.8738 (mp) outliers start: 50 outliers final: 30 residues processed: 387 average time/residue: 0.3234 time to fit residues: 185.9788 Evaluate side-chains 378 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 344 time to evaluate : 2.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 92 THR Chi-restraints excluded: chain Q residue 139 ILE Chi-restraints excluded: chain Q residue 184 LEU Chi-restraints excluded: chain Q residue 223 ILE Chi-restraints excluded: chain Q residue 409 ILE Chi-restraints excluded: chain Q residue 422 LEU Chi-restraints excluded: chain Q residue 436 THR Chi-restraints excluded: chain Q residue 566 VAL Chi-restraints excluded: chain Q residue 702 VAL Chi-restraints excluded: chain Q residue 727 LEU Chi-restraints excluded: chain Q residue 736 ILE Chi-restraints excluded: chain Q residue 740 VAL Chi-restraints excluded: chain Q residue 775 PHE Chi-restraints excluded: chain Q residue 860 ILE Chi-restraints excluded: chain R residue 422 LEU Chi-restraints excluded: chain R residue 516 LYS Chi-restraints excluded: chain R residue 592 ASN Chi-restraints excluded: chain R residue 609 THR Chi-restraints excluded: chain R residue 624 ILE Chi-restraints excluded: chain R residue 689 VAL Chi-restraints excluded: chain R residue 739 CYS Chi-restraints excluded: chain R residue 836 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 175 optimal weight: 0.6980 chunk 119 optimal weight: 0.2980 chunk 3 optimal weight: 0.2980 chunk 156 optimal weight: 0.0980 chunk 86 optimal weight: 0.6980 chunk 179 optimal weight: 0.9990 chunk 145 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 107 optimal weight: 0.5980 chunk 189 optimal weight: 0.0030 chunk 53 optimal weight: 0.8980 overall best weight: 0.2590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17907 Z= 0.185 Angle : 0.515 10.080 24328 Z= 0.270 Chirality : 0.042 0.153 2790 Planarity : 0.004 0.049 3056 Dihedral : 6.828 71.327 2791 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.00 % Allowed : 13.98 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.17), residues: 2182 helix: 0.92 (0.16), residues: 926 sheet: -1.29 (0.26), residues: 360 loop : -0.66 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP Q 299 HIS 0.005 0.001 HIS B 311 PHE 0.032 0.001 PHE A 100 TYR 0.020 0.001 TYR R 744 ARG 0.003 0.000 ARG Q 551 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 361 time to evaluate : 1.909 Fit side-chains revert: symmetry clash REVERT: Q 702 VAL cc_start: 0.7008 (OUTLIER) cc_final: 0.6663 (t) REVERT: R 248 ASP cc_start: 0.6501 (m-30) cc_final: 0.6140 (m-30) REVERT: R 277 GLU cc_start: 0.7941 (tt0) cc_final: 0.7505 (tt0) REVERT: R 422 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7574 (mp) REVERT: R 679 LEU cc_start: 0.6759 (tp) cc_final: 0.6407 (mt) REVERT: A 106 ILE cc_start: 0.8290 (mm) cc_final: 0.7958 (mm) REVERT: A 122 LEU cc_start: 0.7842 (tp) cc_final: 0.7558 (tp) REVERT: A 135 ARG cc_start: 0.8032 (ttp80) cc_final: 0.7467 (ttp80) REVERT: A 190 LYS cc_start: 0.7822 (mtpt) cc_final: 0.7564 (ttmm) REVERT: A 192 PHE cc_start: 0.6690 (t80) cc_final: 0.6396 (t80) REVERT: A 234 ILE cc_start: 0.8895 (OUTLIER) cc_final: 0.8620 (mp) REVERT: A 235 ILE cc_start: 0.8667 (mm) cc_final: 0.8347 (mp) REVERT: B 36 ASN cc_start: 0.5189 (m-40) cc_final: 0.4810 (p0) REVERT: B 198 LEU cc_start: 0.8934 (mm) cc_final: 0.8715 (mp) outliers start: 36 outliers final: 27 residues processed: 379 average time/residue: 0.3213 time to fit residues: 182.3124 Evaluate side-chains 369 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 339 time to evaluate : 1.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 139 ILE Chi-restraints excluded: chain Q residue 223 ILE Chi-restraints excluded: chain Q residue 409 ILE Chi-restraints excluded: chain Q residue 422 LEU Chi-restraints excluded: chain Q residue 436 THR Chi-restraints excluded: chain Q residue 485 LEU Chi-restraints excluded: chain Q residue 702 VAL Chi-restraints excluded: chain Q residue 727 LEU Chi-restraints excluded: chain Q residue 736 ILE Chi-restraints excluded: chain Q residue 775 PHE Chi-restraints excluded: chain Q residue 860 ILE Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 422 LEU Chi-restraints excluded: chain R residue 592 ASN Chi-restraints excluded: chain R residue 609 THR Chi-restraints excluded: chain R residue 624 ILE Chi-restraints excluded: chain R residue 836 VAL Chi-restraints excluded: chain R residue 848 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 70 optimal weight: 1.9990 chunk 189 optimal weight: 0.0970 chunk 41 optimal weight: 0.6980 chunk 123 optimal weight: 0.0470 chunk 52 optimal weight: 0.9980 chunk 210 optimal weight: 5.9990 chunk 175 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 69 optimal weight: 0.0980 chunk 110 optimal weight: 0.9990 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17907 Z= 0.222 Angle : 0.518 9.169 24328 Z= 0.272 Chirality : 0.042 0.151 2790 Planarity : 0.004 0.046 3056 Dihedral : 6.687 70.405 2791 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.33 % Allowed : 14.71 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.18), residues: 2182 helix: 1.02 (0.16), residues: 926 sheet: -1.27 (0.26), residues: 378 loop : -0.67 (0.20), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Q 299 HIS 0.004 0.001 HIS Q 466 PHE 0.029 0.001 PHE A 100 TYR 0.020 0.001 TYR R 744 ARG 0.005 0.000 ARG R 535 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 359 time to evaluate : 1.961 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 203 TYR cc_start: 0.7989 (t80) cc_final: 0.7775 (t80) REVERT: R 248 ASP cc_start: 0.6492 (m-30) cc_final: 0.6131 (m-30) REVERT: R 277 GLU cc_start: 0.7923 (tt0) cc_final: 0.7485 (tt0) REVERT: R 422 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7568 (mp) REVERT: R 526 GLU cc_start: 0.6773 (pp20) cc_final: 0.6493 (pp20) REVERT: R 679 LEU cc_start: 0.6796 (tp) cc_final: 0.6438 (mt) REVERT: A 106 ILE cc_start: 0.8345 (mm) cc_final: 0.7948 (mm) REVERT: A 122 LEU cc_start: 0.7825 (tp) cc_final: 0.7562 (tp) REVERT: A 192 PHE cc_start: 0.6670 (t80) cc_final: 0.6368 (t80) REVERT: A 234 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8663 (mp) REVERT: B 198 LEU cc_start: 0.8934 (mm) cc_final: 0.8714 (mp) REVERT: B 285 LEU cc_start: 0.8797 (tp) cc_final: 0.8417 (tt) outliers start: 42 outliers final: 28 residues processed: 383 average time/residue: 0.3219 time to fit residues: 184.8415 Evaluate side-chains 371 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 341 time to evaluate : 1.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 139 ILE Chi-restraints excluded: chain Q residue 223 ILE Chi-restraints excluded: chain Q residue 422 LEU Chi-restraints excluded: chain Q residue 436 THR Chi-restraints excluded: chain Q residue 485 LEU Chi-restraints excluded: chain Q residue 727 LEU Chi-restraints excluded: chain Q residue 736 ILE Chi-restraints excluded: chain Q residue 775 PHE Chi-restraints excluded: chain Q residue 860 ILE Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 422 LEU Chi-restraints excluded: chain R residue 592 ASN Chi-restraints excluded: chain R residue 609 THR Chi-restraints excluded: chain R residue 624 ILE Chi-restraints excluded: chain R residue 689 VAL Chi-restraints excluded: chain R residue 738 ILE Chi-restraints excluded: chain R residue 739 CYS Chi-restraints excluded: chain R residue 836 VAL Chi-restraints excluded: chain R residue 848 LEU Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 203 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 154 optimal weight: 0.2980 chunk 119 optimal weight: 0.5980 chunk 177 optimal weight: 4.9990 chunk 117 optimal weight: 0.4980 chunk 210 optimal weight: 5.9990 chunk 131 optimal weight: 0.7980 chunk 128 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 17907 Z= 0.298 Angle : 0.548 8.756 24328 Z= 0.288 Chirality : 0.043 0.143 2790 Planarity : 0.004 0.050 3056 Dihedral : 6.741 71.131 2791 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.55 % Allowed : 15.15 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.17), residues: 2182 helix: 0.92 (0.16), residues: 931 sheet: -1.29 (0.25), residues: 378 loop : -0.73 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 169 HIS 0.006 0.001 HIS Q 466 PHE 0.025 0.002 PHE A 100 TYR 0.020 0.002 TYR R 744 ARG 0.004 0.000 ARG R 535 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 349 time to evaluate : 1.909 Fit side-chains REVERT: Q 270 PHE cc_start: 0.7291 (OUTLIER) cc_final: 0.6871 (m-80) REVERT: Q 561 CYS cc_start: 0.5105 (m) cc_final: 0.4893 (m) REVERT: R 216 ASP cc_start: 0.7178 (p0) cc_final: 0.6927 (p0) REVERT: R 248 ASP cc_start: 0.6533 (m-30) cc_final: 0.6156 (m-30) REVERT: R 277 GLU cc_start: 0.7948 (tt0) cc_final: 0.7491 (tt0) REVERT: R 282 GLU cc_start: 0.6736 (tp30) cc_final: 0.6341 (tp30) REVERT: R 422 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7542 (mp) REVERT: R 526 GLU cc_start: 0.6790 (pp20) cc_final: 0.6492 (pp20) REVERT: R 795 ARG cc_start: 0.7608 (ptt-90) cc_final: 0.7328 (ptt-90) REVERT: A 122 LEU cc_start: 0.7860 (tp) cc_final: 0.7597 (tp) REVERT: A 192 PHE cc_start: 0.6689 (t80) cc_final: 0.6386 (t80) REVERT: A 234 ILE cc_start: 0.8876 (OUTLIER) cc_final: 0.8628 (mp) REVERT: A 235 ILE cc_start: 0.8732 (mm) cc_final: 0.8512 (mp) REVERT: B 36 ASN cc_start: 0.5199 (m-40) cc_final: 0.4874 (p0) REVERT: B 198 LEU cc_start: 0.8946 (mm) cc_final: 0.8723 (mp) REVERT: B 285 LEU cc_start: 0.8815 (tp) cc_final: 0.8424 (tt) outliers start: 46 outliers final: 34 residues processed: 373 average time/residue: 0.3209 time to fit residues: 177.9785 Evaluate side-chains 375 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 338 time to evaluate : 2.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 92 THR Chi-restraints excluded: chain Q residue 139 ILE Chi-restraints excluded: chain Q residue 184 LEU Chi-restraints excluded: chain Q residue 223 ILE Chi-restraints excluded: chain Q residue 270 PHE Chi-restraints excluded: chain Q residue 409 ILE Chi-restraints excluded: chain Q residue 422 LEU Chi-restraints excluded: chain Q residue 436 THR Chi-restraints excluded: chain Q residue 485 LEU Chi-restraints excluded: chain Q residue 566 VAL Chi-restraints excluded: chain Q residue 727 LEU Chi-restraints excluded: chain Q residue 736 ILE Chi-restraints excluded: chain Q residue 757 GLU Chi-restraints excluded: chain Q residue 775 PHE Chi-restraints excluded: chain Q residue 860 ILE Chi-restraints excluded: chain R residue 24 GLN Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 422 LEU Chi-restraints excluded: chain R residue 478 THR Chi-restraints excluded: chain R residue 592 ASN Chi-restraints excluded: chain R residue 609 THR Chi-restraints excluded: chain R residue 624 ILE Chi-restraints excluded: chain R residue 689 VAL Chi-restraints excluded: chain R residue 739 CYS Chi-restraints excluded: chain R residue 836 VAL Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 129 optimal weight: 0.6980 chunk 83 optimal weight: 0.9990 chunk 125 optimal weight: 0.0980 chunk 63 optimal weight: 0.2980 chunk 41 optimal weight: 1.9990 chunk 40 optimal weight: 0.4980 chunk 133 optimal weight: 1.9990 chunk 143 optimal weight: 0.0770 chunk 103 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 165 optimal weight: 2.9990 overall best weight: 0.3138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17907 Z= 0.201 Angle : 0.523 11.942 24328 Z= 0.273 Chirality : 0.042 0.143 2790 Planarity : 0.004 0.046 3056 Dihedral : 6.583 70.166 2791 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.22 % Allowed : 15.65 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.18), residues: 2182 helix: 1.03 (0.16), residues: 932 sheet: -1.25 (0.25), residues: 383 loop : -0.66 (0.21), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 169 HIS 0.004 0.001 HIS Q 466 PHE 0.025 0.001 PHE A 100 TYR 0.020 0.001 TYR Q 510 ARG 0.003 0.000 ARG R 535 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 339 time to evaluate : 1.915 Fit side-chains REVERT: Q 270 PHE cc_start: 0.7241 (OUTLIER) cc_final: 0.6882 (m-80) REVERT: Q 433 ASP cc_start: 0.5758 (m-30) cc_final: 0.5522 (m-30) REVERT: Q 561 CYS cc_start: 0.5061 (m) cc_final: 0.4846 (m) REVERT: R 216 ASP cc_start: 0.7183 (p0) cc_final: 0.6928 (p0) REVERT: R 248 ASP cc_start: 0.6505 (m-30) cc_final: 0.6111 (m-30) REVERT: R 277 GLU cc_start: 0.7928 (tt0) cc_final: 0.7465 (tt0) REVERT: R 422 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7514 (mp) REVERT: R 526 GLU cc_start: 0.6760 (pp20) cc_final: 0.6463 (pp20) REVERT: R 592 ASN cc_start: 0.7972 (OUTLIER) cc_final: 0.7688 (p0) REVERT: A 122 LEU cc_start: 0.7834 (tp) cc_final: 0.7574 (tp) REVERT: A 192 PHE cc_start: 0.6641 (t80) cc_final: 0.6324 (t80) REVERT: A 234 ILE cc_start: 0.8873 (OUTLIER) cc_final: 0.8648 (mp) REVERT: A 235 ILE cc_start: 0.8695 (mm) cc_final: 0.8481 (mp) REVERT: B 36 ASN cc_start: 0.5076 (m-40) cc_final: 0.4805 (p0) REVERT: B 198 LEU cc_start: 0.8922 (mm) cc_final: 0.8698 (mp) REVERT: B 285 LEU cc_start: 0.8803 (tp) cc_final: 0.8425 (tt) outliers start: 40 outliers final: 30 residues processed: 359 average time/residue: 0.3220 time to fit residues: 172.8042 Evaluate side-chains 375 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 341 time to evaluate : 1.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 139 ILE Chi-restraints excluded: chain Q residue 223 ILE Chi-restraints excluded: chain Q residue 270 PHE Chi-restraints excluded: chain Q residue 409 ILE Chi-restraints excluded: chain Q residue 422 LEU Chi-restraints excluded: chain Q residue 436 THR Chi-restraints excluded: chain Q residue 485 LEU Chi-restraints excluded: chain Q residue 727 LEU Chi-restraints excluded: chain Q residue 736 ILE Chi-restraints excluded: chain Q residue 757 GLU Chi-restraints excluded: chain Q residue 775 PHE Chi-restraints excluded: chain Q residue 860 ILE Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 422 LEU Chi-restraints excluded: chain R residue 478 THR Chi-restraints excluded: chain R residue 592 ASN Chi-restraints excluded: chain R residue 609 THR Chi-restraints excluded: chain R residue 624 ILE Chi-restraints excluded: chain R residue 739 CYS Chi-restraints excluded: chain R residue 836 VAL Chi-restraints excluded: chain R residue 848 LEU Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 191 optimal weight: 3.9990 chunk 201 optimal weight: 0.8980 chunk 183 optimal weight: 0.9990 chunk 195 optimal weight: 0.9980 chunk 117 optimal weight: 0.0000 chunk 85 optimal weight: 0.0060 chunk 153 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 176 optimal weight: 4.9990 chunk 185 optimal weight: 0.9980 chunk 128 optimal weight: 0.8980 overall best weight: 0.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17907 Z= 0.281 Angle : 0.550 13.212 24328 Z= 0.288 Chirality : 0.043 0.143 2790 Planarity : 0.004 0.068 3056 Dihedral : 6.579 70.316 2791 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.28 % Allowed : 15.93 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.17), residues: 2182 helix: 0.97 (0.16), residues: 931 sheet: -1.21 (0.25), residues: 373 loop : -0.68 (0.21), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 675 HIS 0.005 0.001 HIS B 54 PHE 0.023 0.002 PHE R 270 TYR 0.019 0.002 TYR R 744 ARG 0.005 0.000 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 349 time to evaluate : 1.933 Fit side-chains REVERT: Q 270 PHE cc_start: 0.7282 (OUTLIER) cc_final: 0.6907 (m-80) REVERT: Q 561 CYS cc_start: 0.5041 (m) cc_final: 0.4803 (m) REVERT: Q 564 GLU cc_start: 0.6409 (OUTLIER) cc_final: 0.6087 (pt0) REVERT: R 216 ASP cc_start: 0.7185 (p0) cc_final: 0.6953 (p0) REVERT: R 248 ASP cc_start: 0.6509 (m-30) cc_final: 0.6121 (m-30) REVERT: R 277 GLU cc_start: 0.7931 (tt0) cc_final: 0.7464 (tt0) REVERT: R 422 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7550 (mp) REVERT: R 526 GLU cc_start: 0.6794 (pp20) cc_final: 0.6486 (pp20) REVERT: R 679 LEU cc_start: 0.6074 (tt) cc_final: 0.5743 (mt) REVERT: R 795 ARG cc_start: 0.7598 (ptt-90) cc_final: 0.7343 (ptt-90) REVERT: A 106 ILE cc_start: 0.8324 (mm) cc_final: 0.8006 (mm) REVERT: A 122 LEU cc_start: 0.7850 (tp) cc_final: 0.7590 (tp) REVERT: A 192 PHE cc_start: 0.6670 (t80) cc_final: 0.6343 (t80) REVERT: A 234 ILE cc_start: 0.8880 (OUTLIER) cc_final: 0.8656 (mp) REVERT: A 235 ILE cc_start: 0.8717 (mm) cc_final: 0.8510 (mp) REVERT: B 36 ASN cc_start: 0.5073 (m-40) cc_final: 0.4828 (p0) REVERT: B 198 LEU cc_start: 0.8952 (mm) cc_final: 0.8725 (mp) REVERT: B 261 LEU cc_start: 0.7173 (mm) cc_final: 0.6844 (mp) REVERT: B 285 LEU cc_start: 0.8806 (tp) cc_final: 0.8427 (tt) REVERT: B 311 HIS cc_start: 0.6525 (m-70) cc_final: 0.6075 (t-90) outliers start: 41 outliers final: 31 residues processed: 370 average time/residue: 0.3200 time to fit residues: 176.7960 Evaluate side-chains 375 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 340 time to evaluate : 2.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 139 ILE Chi-restraints excluded: chain Q residue 223 ILE Chi-restraints excluded: chain Q residue 270 PHE Chi-restraints excluded: chain Q residue 409 ILE Chi-restraints excluded: chain Q residue 422 LEU Chi-restraints excluded: chain Q residue 436 THR Chi-restraints excluded: chain Q residue 485 LEU Chi-restraints excluded: chain Q residue 564 GLU Chi-restraints excluded: chain Q residue 727 LEU Chi-restraints excluded: chain Q residue 736 ILE Chi-restraints excluded: chain Q residue 757 GLU Chi-restraints excluded: chain Q residue 775 PHE Chi-restraints excluded: chain Q residue 860 ILE Chi-restraints excluded: chain R residue 24 GLN Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 422 LEU Chi-restraints excluded: chain R residue 478 THR Chi-restraints excluded: chain R residue 609 THR Chi-restraints excluded: chain R residue 624 ILE Chi-restraints excluded: chain R residue 739 CYS Chi-restraints excluded: chain R residue 836 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 207 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 98 optimal weight: 0.0770 chunk 143 optimal weight: 0.3980 chunk 217 optimal weight: 0.0670 chunk 199 optimal weight: 0.9990 chunk 172 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 133 optimal weight: 0.8980 chunk 106 optimal weight: 0.0970 chunk 137 optimal weight: 0.9990 overall best weight: 0.2874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17907 Z= 0.196 Angle : 0.531 12.884 24328 Z= 0.277 Chirality : 0.042 0.142 2790 Planarity : 0.004 0.066 3056 Dihedral : 6.463 69.370 2791 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.00 % Allowed : 16.26 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.18), residues: 2182 helix: 1.09 (0.16), residues: 932 sheet: -1.15 (0.26), residues: 372 loop : -0.66 (0.20), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 169 HIS 0.007 0.001 HIS B 54 PHE 0.022 0.001 PHE A 100 TYR 0.018 0.001 TYR R 744 ARG 0.010 0.000 ARG A 208 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 339 time to evaluate : 1.679 Fit side-chains revert: symmetry clash REVERT: Q 270 PHE cc_start: 0.7239 (OUTLIER) cc_final: 0.6851 (m-80) REVERT: Q 433 ASP cc_start: 0.5771 (m-30) cc_final: 0.5450 (m-30) REVERT: R 216 ASP cc_start: 0.7188 (p0) cc_final: 0.6940 (p0) REVERT: R 248 ASP cc_start: 0.6501 (m-30) cc_final: 0.6148 (m-30) REVERT: R 277 GLU cc_start: 0.7913 (tt0) cc_final: 0.7462 (tt0) REVERT: R 282 GLU cc_start: 0.6715 (tp30) cc_final: 0.6331 (tp30) REVERT: R 422 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7558 (mp) REVERT: R 526 GLU cc_start: 0.6762 (pp20) cc_final: 0.6321 (pp20) REVERT: R 679 LEU cc_start: 0.6097 (tt) cc_final: 0.5808 (mt) REVERT: A 106 ILE cc_start: 0.8316 (mm) cc_final: 0.8014 (mm) REVERT: A 122 LEU cc_start: 0.7820 (tp) cc_final: 0.7561 (tp) REVERT: A 192 PHE cc_start: 0.6633 (t80) cc_final: 0.6309 (t80) REVERT: A 234 ILE cc_start: 0.8875 (OUTLIER) cc_final: 0.8664 (mp) REVERT: B 198 LEU cc_start: 0.8925 (mm) cc_final: 0.8689 (mp) REVERT: B 285 LEU cc_start: 0.8802 (tp) cc_final: 0.8428 (tt) REVERT: B 311 HIS cc_start: 0.6411 (m-70) cc_final: 0.6077 (t-90) outliers start: 36 outliers final: 28 residues processed: 357 average time/residue: 0.3395 time to fit residues: 182.4097 Evaluate side-chains 367 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 336 time to evaluate : 2.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 139 ILE Chi-restraints excluded: chain Q residue 223 ILE Chi-restraints excluded: chain Q residue 270 PHE Chi-restraints excluded: chain Q residue 409 ILE Chi-restraints excluded: chain Q residue 422 LEU Chi-restraints excluded: chain Q residue 485 LEU Chi-restraints excluded: chain Q residue 727 LEU Chi-restraints excluded: chain Q residue 736 ILE Chi-restraints excluded: chain Q residue 757 GLU Chi-restraints excluded: chain Q residue 775 PHE Chi-restraints excluded: chain Q residue 860 ILE Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 422 LEU Chi-restraints excluded: chain R residue 478 THR Chi-restraints excluded: chain R residue 609 THR Chi-restraints excluded: chain R residue 624 ILE Chi-restraints excluded: chain R residue 739 CYS Chi-restraints excluded: chain R residue 836 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/programs/real_space_refine.py", line 213, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.5424 > 50: distance: 8 - 13: 16.356 distance: 13 - 14: 24.472 distance: 13 - 19: 49.994 distance: 14 - 15: 26.849 distance: 14 - 17: 23.320 distance: 15 - 16: 18.375 distance: 15 - 20: 55.788 distance: 17 - 18: 40.025 distance: 18 - 19: 40.969 distance: 21 - 22: 38.266 distance: 22 - 23: 38.253 distance: 24 - 25: 41.302 distance: 25 - 26: 40.600 distance: 26 - 27: 6.199 distance: 29 - 30: 40.782 distance: 30 - 33: 40.792 distance: 31 - 34: 27.615 distance: 34 - 35: 13.584 distance: 35 - 38: 39.338 distance: 36 - 39: 28.410 distance: 39 - 40: 41.994 distance: 41 - 42: 31.268 distance: 41 - 46: 14.390 distance: 43 - 44: 32.434 distance: 43 - 45: 3.955 distance: 46 - 47: 41.138 distance: 46 - 52: 13.192 distance: 47 - 48: 32.420 distance: 47 - 50: 37.056 distance: 48 - 49: 26.831 distance: 48 - 53: 41.665 distance: 50 - 51: 32.294 distance: 51 - 52: 8.170 distance: 53 - 54: 25.947 distance: 54 - 55: 35.152 distance: 54 - 57: 42.891 distance: 55 - 56: 7.715 distance: 55 - 62: 43.622 distance: 57 - 58: 15.286 distance: 58 - 59: 30.874 distance: 59 - 60: 40.080 distance: 62 - 63: 22.954 distance: 62 - 68: 33.001 distance: 63 - 64: 27.450 distance: 63 - 66: 39.631 distance: 64 - 65: 26.388 distance: 64 - 69: 26.973 distance: 66 - 67: 22.037 distance: 67 - 68: 18.243 distance: 69 - 70: 27.982 distance: 70 - 71: 28.198 distance: 71 - 73: 6.833 distance: 73 - 74: 8.748 distance: 74 - 75: 8.920 distance: 75 - 76: 63.960 distance: 75 - 78: 29.684