Starting phenix.real_space_refine on Tue Feb 20 22:05:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f59_31462/02_2024/7f59_31462_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f59_31462/02_2024/7f59_31462.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f59_31462/02_2024/7f59_31462.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f59_31462/02_2024/7f59_31462.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f59_31462/02_2024/7f59_31462_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f59_31462/02_2024/7f59_31462_neut_updated.pdb" } resolution = 4.2 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= 0.006 sd= 0.101 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: 4 Type Number sf(0) Gaussians S 171 5.16 5 C 18558 2.51 5 N 4806 2.21 5 O 5437 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 187": "OE1" <-> "OE2" Residue "A GLU 415": "OE1" <-> "OE2" Residue "A ARG 503": "NH1" <-> "NH2" Residue "A TYR 774": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 90": "OE1" <-> "OE2" Residue "B PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 524": "OE1" <-> "OE2" Residue "B GLU 603": "OE1" <-> "OE2" Residue "B GLU 665": "OE1" <-> "OE2" Residue "C GLU 460": "OE1" <-> "OE2" Residue "C TYR 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 524": "OE1" <-> "OE2" Residue "C GLU 681": "OE1" <-> "OE2" Residue "C GLU 796": "OE1" <-> "OE2" Residue "C GLU 841": "OE1" <-> "OE2" Residue "D GLU 440": "OE1" <-> "OE2" Residue "D GLU 460": "OE1" <-> "OE2" Residue "D GLU 479": "OE1" <-> "OE2" Residue "D GLU 625": "OE1" <-> "OE2" Residue "D GLU 743": "OE1" <-> "OE2" Residue "E GLU 146": "OE1" <-> "OE2" Residue "E GLU 148": "OE1" <-> "OE2" Residue "E ARG 189": "NH1" <-> "NH2" Residue "E ARG 281": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 28972 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 6604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 835, 6604 Classifications: {'peptide': 835} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 33, 'TRANS': 801} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 6572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 831, 6572 Classifications: {'peptide': 831} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 33, 'TRANS': 797} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 6614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 835, 6614 Classifications: {'peptide': 835} Link IDs: {'PTRANS': 33, 'TRANS': 801} Chain: "D" Number of atoms: 6471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 818, 6471 Classifications: {'peptide': 818} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 33, 'TRANS': 784} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "E" Number of atoms: 2441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2441 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 15, 'TRANS': 293} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'PGT': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PGT:plan-1': 1, 'PGT:plan-2': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 14.37, per 1000 atoms: 0.50 Number of scatterers: 28972 At special positions: 0 Unit cell: (125.12, 142.8, 220.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 171 16.00 O 5437 8.00 N 4806 7.00 C 18558 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 347 " distance=2.38 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 347 " distance=2.22 Simple disulfide: pdb=" SG CYS C 96 " - pdb=" SG CYS C 347 " distance=2.39 Simple disulfide: pdb=" SG CYS D 96 " - pdb=" SG CYS D 347 " distance=2.29 Simple disulfide: pdb=" SG CYS E 45 " - pdb=" SG CYS E 72 " distance=2.37 Simple disulfide: pdb=" SG CYS E 177 " - pdb=" SG CYS E 207 " distance=2.04 Simple disulfide: pdb=" SG CYS E 234 " - pdb=" SG CYS E 256 " distance=1.99 Simple disulfide: pdb=" SG CYS E 297 " - pdb=" SG CYS E 309 " distance=2.03 Simple disulfide: pdb=" SG CYS E 304 " - pdb=" SG CYS E 322 " distance=2.33 Simple disulfide: pdb=" SG CYS E 316 " - pdb=" SG CYS E 331 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " NAG-ASN " NAG A1001 " - " ASN A 275 " " NAG B1001 " - " ASN B 275 " " NAG B1002 " - " ASN B 412 " " NAG B1003 " - " ASN B 546 " " NAG D1001 " - " ASN D 275 " " NAG D1002 " - " ASN D 412 " " NAG D1003 " - " ASN D 546 " " NAG F 1 " - " ASN A 378 " " NAG G 1 " - " ASN B 378 " " NAG H 1 " - " ASN C 378 " " NAG I 1 " - " ASN D 378 " Time building additional restraints: 11.41 Conformation dependent library (CDL) restraints added in 5.0 seconds 7228 Ramachandran restraints generated. 3614 Oldfield, 0 Emsley, 3614 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6768 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 117 helices and 35 sheets defined 38.7% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.49 Creating SS restraints... Processing helix chain 'A' and resid 52 through 66 Processing helix chain 'A' and resid 88 through 101 Processing helix chain 'A' and resid 112 through 125 removed outlier: 3.983A pdb=" N ALA A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA A 124 " --> pdb=" O SER A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 167 Processing helix chain 'A' and resid 179 through 184 Processing helix chain 'A' and resid 186 through 193 removed outlier: 3.591A pdb=" N ALA A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) Proline residue: A 192 - end of helix Processing helix chain 'A' and resid 208 through 221 Proline residue: A 213 - end of helix Processing helix chain 'A' and resid 232 through 244 removed outlier: 4.331A pdb=" N GLN A 241 " --> pdb=" O GLY A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 272 Processing helix chain 'A' and resid 287 through 301 removed outlier: 3.701A pdb=" N LEU A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 318 through 336 removed outlier: 3.784A pdb=" N VAL A 327 " --> pdb=" O MET A 323 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N HIS A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N GLN A 336 " --> pdb=" O VAL A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 365 removed outlier: 3.653A pdb=" N MET A 360 " --> pdb=" O GLY A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 419 Processing helix chain 'A' and resid 462 through 474 Processing helix chain 'A' and resid 500 through 506 Processing helix chain 'A' and resid 521 through 526 Processing helix chain 'A' and resid 561 through 583 Processing helix chain 'A' and resid 608 through 620 Processing helix chain 'A' and resid 631 through 664 removed outlier: 4.217A pdb=" N VAL A 636 " --> pdb=" O SER A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 676 Processing helix chain 'A' and resid 690 through 696 Processing helix chain 'A' and resid 700 through 712 Processing helix chain 'A' and resid 722 through 730 Processing helix chain 'A' and resid 739 through 748 Processing helix chain 'A' and resid 774 through 788 Processing helix chain 'A' and resid 790 through 798 Processing helix chain 'A' and resid 825 through 850 Processing helix chain 'A' and resid 857 through 865 Processing helix chain 'B' and resid 52 through 66 removed outlier: 4.396A pdb=" N ASN B 65 " --> pdb=" O VAL B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 101 Processing helix chain 'B' and resid 113 through 125 removed outlier: 3.940A pdb=" N ALA B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL B 118 " --> pdb=" O SER B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 167 Processing helix chain 'B' and resid 179 through 190 removed outlier: 5.675A pdb=" N GLU B 187 " --> pdb=" O ARG B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 221 removed outlier: 3.959A pdb=" N LYS B 212 " --> pdb=" O LYS B 209 " (cutoff:3.500A) Proline residue: B 213 - end of helix removed outlier: 3.642A pdb=" N GLY B 221 " --> pdb=" O MET B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 244 removed outlier: 3.951A pdb=" N GLY B 237 " --> pdb=" O GLU B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 263 No H-bonds generated for 'chain 'B' and resid 261 through 263' Processing helix chain 'B' and resid 267 through 272 removed outlier: 3.533A pdb=" N ARG B 270 " --> pdb=" O GLU B 267 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N TYR B 271 " --> pdb=" O PRO B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 302 removed outlier: 3.501A pdb=" N GLU B 299 " --> pdb=" O LYS B 295 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N GLN B 302 " --> pdb=" O MET B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 309 No H-bonds generated for 'chain 'B' and resid 307 through 309' Processing helix chain 'B' and resid 318 through 334 removed outlier: 3.665A pdb=" N VAL B 327 " --> pdb=" O MET B 323 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N HIS B 328 " --> pdb=" O TYR B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 363 removed outlier: 3.581A pdb=" N LEU B 362 " --> pdb=" O ARG B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 418 Processing helix chain 'B' and resid 462 through 474 Processing helix chain 'B' and resid 501 through 506 Processing helix chain 'B' and resid 521 through 526 removed outlier: 3.646A pdb=" N VAL B 526 " --> pdb=" O VAL B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 555 No H-bonds generated for 'chain 'B' and resid 552 through 555' Processing helix chain 'B' and resid 561 through 584 Processing helix chain 'B' and resid 594 through 596 No H-bonds generated for 'chain 'B' and resid 594 through 596' Processing helix chain 'B' and resid 608 through 619 Processing helix chain 'B' and resid 631 through 660 removed outlier: 3.734A pdb=" N VAL B 636 " --> pdb=" O SER B 632 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR B 660 " --> pdb=" O ALA B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 676 Processing helix chain 'B' and resid 689 through 694 Processing helix chain 'B' and resid 702 through 711 Processing helix chain 'B' and resid 721 through 730 Processing helix chain 'B' and resid 739 through 746 Processing helix chain 'B' and resid 774 through 788 Processing helix chain 'B' and resid 790 through 799 Processing helix chain 'B' and resid 817 through 819 No H-bonds generated for 'chain 'B' and resid 817 through 819' Processing helix chain 'B' and resid 821 through 849 Processing helix chain 'B' and resid 856 through 862 Processing helix chain 'C' and resid 52 through 66 removed outlier: 3.624A pdb=" N VAL C 61 " --> pdb=" O PHE C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 101 Processing helix chain 'C' and resid 112 through 124 removed outlier: 4.648A pdb=" N ALA C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 167 Processing helix chain 'C' and resid 179 through 193 removed outlier: 5.327A pdb=" N GLU C 187 " --> pdb=" O ARG C 184 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LYS C 190 " --> pdb=" O GLU C 187 " (cutoff:3.500A) Proline residue: C 192 - end of helix Processing helix chain 'C' and resid 211 through 221 Processing helix chain 'C' and resid 232 through 244 removed outlier: 3.820A pdb=" N GLN C 241 " --> pdb=" O GLY C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 268 No H-bonds generated for 'chain 'C' and resid 266 through 268' Processing helix chain 'C' and resid 287 through 300 Processing helix chain 'C' and resid 318 through 336 removed outlier: 3.559A pdb=" N VAL C 327 " --> pdb=" O MET C 323 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N HIS C 328 " --> pdb=" O TYR C 324 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLN C 336 " --> pdb=" O VAL C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 364 removed outlier: 3.581A pdb=" N SER C 361 " --> pdb=" O THR C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 457 No H-bonds generated for 'chain 'C' and resid 455 through 457' Processing helix chain 'C' and resid 462 through 474 Processing helix chain 'C' and resid 500 through 506 Processing helix chain 'C' and resid 521 through 526 Processing helix chain 'C' and resid 554 through 558 Proline residue: C 558 - end of helix Processing helix chain 'C' and resid 563 through 582 Processing helix chain 'C' and resid 608 through 620 Processing helix chain 'C' and resid 631 through 663 Processing helix chain 'C' and resid 671 through 676 Processing helix chain 'C' and resid 690 through 695 Processing helix chain 'C' and resid 700 through 712 Processing helix chain 'C' and resid 721 through 730 Processing helix chain 'C' and resid 739 through 748 Processing helix chain 'C' and resid 774 through 787 Processing helix chain 'C' and resid 790 through 798 Processing helix chain 'C' and resid 825 through 847 Processing helix chain 'C' and resid 857 through 865 Processing helix chain 'D' and resid 52 through 66 removed outlier: 3.959A pdb=" N ASN D 65 " --> pdb=" O VAL D 61 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG D 66 " --> pdb=" O ASN D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 100 Processing helix chain 'D' and resid 112 through 123 Processing helix chain 'D' and resid 153 through 167 removed outlier: 4.512A pdb=" N ARG D 158 " --> pdb=" O SER D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 193 removed outlier: 5.185A pdb=" N GLU D 187 " --> pdb=" O ARG D 184 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS D 190 " --> pdb=" O GLU D 187 " (cutoff:3.500A) Proline residue: D 192 - end of helix Processing helix chain 'D' and resid 208 through 221 removed outlier: 4.551A pdb=" N LYS D 212 " --> pdb=" O LYS D 209 " (cutoff:3.500A) Proline residue: D 213 - end of helix Processing helix chain 'D' and resid 232 through 244 removed outlier: 3.940A pdb=" N GLY D 237 " --> pdb=" O GLU D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 263 No H-bonds generated for 'chain 'D' and resid 261 through 263' Processing helix chain 'D' and resid 267 through 269 No H-bonds generated for 'chain 'D' and resid 267 through 269' Processing helix chain 'D' and resid 287 through 302 removed outlier: 5.835A pdb=" N GLN D 302 " --> pdb=" O MET D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 336 removed outlier: 3.832A pdb=" N HIS D 328 " --> pdb=" O TYR D 324 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ALA D 333 " --> pdb=" O VAL D 329 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLN D 336 " --> pdb=" O VAL D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 356 through 365 removed outlier: 3.921A pdb=" N SER D 361 " --> pdb=" O THR D 357 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU D 362 " --> pdb=" O ARG D 358 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N GLU D 365 " --> pdb=" O SER D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 458 Processing helix chain 'D' and resid 462 through 474 Processing helix chain 'D' and resid 501 through 506 Processing helix chain 'D' and resid 521 through 526 removed outlier: 3.639A pdb=" N LYS D 525 " --> pdb=" O TYR D 521 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL D 526 " --> pdb=" O VAL D 522 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 521 through 526' Processing helix chain 'D' and resid 561 through 583 removed outlier: 4.242A pdb=" N LEU D 568 " --> pdb=" O TRP D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 610 through 619 Processing helix chain 'D' and resid 631 through 660 removed outlier: 3.789A pdb=" N VAL D 636 " --> pdb=" O SER D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 671 through 674 No H-bonds generated for 'chain 'D' and resid 671 through 674' Processing helix chain 'D' and resid 689 through 694 Processing helix chain 'D' and resid 703 through 711 Processing helix chain 'D' and resid 721 through 730 Processing helix chain 'D' and resid 739 through 748 Processing helix chain 'D' and resid 774 through 788 removed outlier: 4.183A pdb=" N ALA D 781 " --> pdb=" O LYS D 777 " (cutoff:3.500A) Processing helix chain 'D' and resid 790 through 799 removed outlier: 3.655A pdb=" N TRP D 798 " --> pdb=" O MET D 794 " (cutoff:3.500A) Processing helix chain 'D' and resid 822 through 849 Processing helix chain 'E' and resid 348 through 371 removed outlier: 3.901A pdb=" N VAL E 368 " --> pdb=" O ILE E 364 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN E 369 " --> pdb=" O SER E 365 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 34 through 36 removed outlier: 3.682A pdb=" N LEU A 36 " --> pdb=" O THR A 75 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 39 through 43 removed outlier: 7.122A pdb=" N ASP A 79 " --> pdb=" O GLY A 40 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N PHE A 42 " --> pdb=" O ASP A 79 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N GLN A 81 " --> pdb=" O PHE A 42 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 129 through 131 Processing sheet with id= D, first strand: chain 'A' and resid 198 through 203 removed outlier: 3.966A pdb=" N LYS A 200 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL A 174 " --> pdb=" O LYS A 200 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR A 176 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N HIS A 225 " --> pdb=" O THR A 173 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N VAL A 175 " --> pdb=" O HIS A 225 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ILE A 227 " --> pdb=" O VAL A 175 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N HIS A 253 " --> pdb=" O VAL A 226 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N PHE A 228 " --> pdb=" O HIS A 253 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE A 255 " --> pdb=" O PHE A 228 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ASN A 275 " --> pdb=" O TYR A 254 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N PHE A 256 " --> pdb=" O ASN A 275 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N THR A 277 " --> pdb=" O PHE A 256 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N MET A 276 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP A 390 " --> pdb=" O ARG A 280 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N SER A 393 " --> pdb=" O LYS A 401 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N LYS A 401 " --> pdb=" O SER A 393 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 432 through 437 removed outlier: 6.698A pdb=" N THR A 477 " --> pdb=" O LEU A 433 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N VAL A 435 " --> pdb=" O THR A 477 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N GLU A 479 " --> pdb=" O VAL A 435 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N THR A 437 " --> pdb=" O GLU A 479 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ARG A 481 " --> pdb=" O THR A 437 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 535 through 537 Processing sheet with id= G, first strand: chain 'A' and resid 736 through 738 removed outlier: 3.817A pdb=" N MET A 737 " --> pdb=" O SER A 539 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER A 539 " --> pdb=" O MET A 737 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE A 540 " --> pdb=" O ILE A 755 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 35 through 38 removed outlier: 6.753A pdb=" N THR B 75 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N PHE B 38 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N THR B 77 " --> pdb=" O PHE B 38 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'B' and resid 129 through 131 Processing sheet with id= J, first strand: chain 'B' and resid 172 through 176 removed outlier: 3.726A pdb=" N TYR B 176 " --> pdb=" O ARG B 202 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 226 through 228 removed outlier: 6.206A pdb=" N ASN B 275 " --> pdb=" O TYR B 254 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N PHE B 256 " --> pdb=" O ASN B 275 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N THR B 277 " --> pdb=" O PHE B 256 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 278 through 280 removed outlier: 3.591A pdb=" N ILE B 392 " --> pdb=" O GLY B 278 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP B 390 " --> pdb=" O ARG B 280 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU B 400 " --> pdb=" O SER B 393 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 403 through 406 removed outlier: 3.640A pdb=" N ASN B 412 " --> pdb=" O THR B 404 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ASP B 406 " --> pdb=" O GLY B 410 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLY B 410 " --> pdb=" O ASP B 406 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 490 through 492 Processing sheet with id= O, first strand: chain 'B' and resid 534 through 536 removed outlier: 4.418A pdb=" N MET B 534 " --> pdb=" O TYR B 764 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 540 through 543 removed outlier: 3.848A pdb=" N ILE B 540 " --> pdb=" O ILE B 755 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 39 through 41 removed outlier: 6.199A pdb=" N ASP C 79 " --> pdb=" O GLY C 40 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'C' and resid 171 through 176 removed outlier: 6.014A pdb=" N ARG C 198 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N VAL C 174 " --> pdb=" O ARG C 198 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LYS C 200 " --> pdb=" O VAL C 174 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N TYR C 176 " --> pdb=" O LYS C 200 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ARG C 202 " --> pdb=" O TYR C 176 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'C' and resid 225 through 228 removed outlier: 6.568A pdb=" N HIS C 253 " --> pdb=" O VAL C 226 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N PHE C 228 " --> pdb=" O HIS C 253 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ILE C 255 " --> pdb=" O PHE C 228 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'C' and resid 368 through 370 Processing sheet with id= U, first strand: chain 'C' and resid 392 through 395 Processing sheet with id= V, first strand: chain 'C' and resid 434 through 437 removed outlier: 5.628A pdb=" N GLU C 479 " --> pdb=" O VAL C 435 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N THR C 437 " --> pdb=" O GLU C 479 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ARG C 481 " --> pdb=" O THR C 437 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'C' and resid 527 through 529 Processing sheet with id= X, first strand: chain 'C' and resid 534 through 536 removed outlier: 3.842A pdb=" N MET C 534 " --> pdb=" O TYR C 764 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 540 through 543 removed outlier: 3.640A pdb=" N ILE C 540 " --> pdb=" O ILE C 755 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR C 542 " --> pdb=" O THR C 753 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 41 through 43 removed outlier: 6.575A pdb=" N GLN D 81 " --> pdb=" O PHE D 42 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'D' and resid 173 through 176 removed outlier: 6.578A pdb=" N LYS D 200 " --> pdb=" O VAL D 174 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N TYR D 176 " --> pdb=" O LYS D 200 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N ARG D 202 " --> pdb=" O TYR D 176 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'D' and resid 253 through 255 removed outlier: 5.980A pdb=" N ASN D 275 " --> pdb=" O TYR D 254 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'D' and resid 388 through 390 removed outlier: 3.654A pdb=" N THR D 404 " --> pdb=" O ASN D 412 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'D' and resid 433 through 435 Processing sheet with id= AE, first strand: chain 'D' and resid 735 through 738 removed outlier: 3.503A pdb=" N MET D 737 " --> pdb=" O SER D 539 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE D 540 " --> pdb=" O ILE D 755 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'E' and resid 54 through 58 removed outlier: 3.739A pdb=" N ILE E 84 " --> pdb=" O SER E 132 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER E 132 " --> pdb=" O ILE E 84 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU E 86 " --> pdb=" O ILE E 130 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ILE E 130 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'E' and resid 72 through 75 removed outlier: 3.608A pdb=" N PHE E 141 " --> pdb=" O CYS E 72 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS E 140 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP E 119 " --> pdb=" O VAL E 107 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ASP E 109 " --> pdb=" O LEU E 117 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LEU E 117 " --> pdb=" O ASP E 109 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'E' and resid 178 through 180 removed outlier: 8.962A pdb=" N PHE E 179 " --> pdb=" O ASP E 206 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ILE E 208 " --> pdb=" O PHE E 179 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL E 239 " --> pdb=" O PHE E 255 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'E' and resid 185 through 188 removed outlier: 3.614A pdb=" N GLY E 186 " --> pdb=" O PHE E 289 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N MET E 287 " --> pdb=" O VAL E 188 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG E 284 " --> pdb=" O GLN E 227 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU E 288 " --> pdb=" O PHE E 223 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N PHE E 223 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N THR E 290 " --> pdb=" O LEU E 221 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N LEU E 221 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE E 219 " --> pdb=" O LEU E 265 " (cutoff:3.500A) 1000 hydrogen bonds defined for protein. 2703 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: 9.87 Time building geometry restraints manager: 12.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 4729 1.30 - 1.43: 7896 1.43 - 1.56: 16714 1.56 - 1.69: 0 1.69 - 1.82: 285 Bond restraints: 29624 Sorted by residual: bond pdb=" C LEU A 445 " pdb=" O LEU A 445 " ideal model delta sigma weight residual 1.234 1.171 0.063 1.51e-02 4.39e+03 1.76e+01 bond pdb=" CA ASP B 260 " pdb=" C ASP B 260 " ideal model delta sigma weight residual 1.524 1.473 0.051 1.40e-02 5.10e+03 1.31e+01 bond pdb=" N ASN A 549 " pdb=" CA ASN A 549 " ideal model delta sigma weight residual 1.454 1.493 -0.039 1.14e-02 7.69e+03 1.16e+01 bond pdb=" C PRO E 295 " pdb=" O PRO E 295 " ideal model delta sigma weight residual 1.243 1.214 0.029 8.50e-03 1.38e+04 1.16e+01 bond pdb=" C GLU B 267 " pdb=" N PRO B 268 " ideal model delta sigma weight residual 1.337 1.305 0.032 9.80e-03 1.04e+04 1.05e+01 ... (remaining 29619 not shown) Histogram of bond angle deviations from ideal: 95.24 - 103.05: 263 103.05 - 110.87: 10721 110.87 - 118.68: 13009 118.68 - 126.50: 15694 126.50 - 134.31: 420 Bond angle restraints: 40107 Sorted by residual: angle pdb=" N PRO E 295 " pdb=" CA PRO E 295 " pdb=" C PRO E 295 " ideal model delta sigma weight residual 110.58 123.04 -12.46 1.07e+00 8.73e-01 1.36e+02 angle pdb=" N CYS E 297 " pdb=" CA CYS E 297 " pdb=" C CYS E 297 " ideal model delta sigma weight residual 110.23 119.43 -9.20 1.45e+00 4.76e-01 4.03e+01 angle pdb=" N THR D 180 " pdb=" CA THR D 180 " pdb=" C THR D 180 " ideal model delta sigma weight residual 112.87 105.31 7.56 1.20e+00 6.94e-01 3.96e+01 angle pdb=" N THR E 298 " pdb=" CA THR E 298 " pdb=" C THR E 298 " ideal model delta sigma weight residual 109.14 100.06 9.08 1.49e+00 4.50e-01 3.71e+01 angle pdb=" C LYS E 198 " pdb=" CA LYS E 198 " pdb=" CB LYS E 198 " ideal model delta sigma weight residual 110.67 119.61 -8.94 1.52e+00 4.33e-01 3.46e+01 ... (remaining 40102 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.65: 16863 21.65 - 43.30: 965 43.30 - 64.95: 70 64.95 - 86.60: 50 86.60 - 108.25: 20 Dihedral angle restraints: 17968 sinusoidal: 7448 harmonic: 10520 Sorted by residual: dihedral pdb=" CB CYS E 45 " pdb=" SG CYS E 45 " pdb=" SG CYS E 72 " pdb=" CB CYS E 72 " ideal model delta sinusoidal sigma weight residual 93.00 36.82 56.18 1 1.00e+01 1.00e-02 4.26e+01 dihedral pdb=" CA PHE B 694 " pdb=" C PHE B 694 " pdb=" N LYS B 695 " pdb=" CA LYS B 695 " ideal model delta harmonic sigma weight residual 180.00 150.13 29.87 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" CA GLU E 328 " pdb=" C GLU E 328 " pdb=" N ASN E 329 " pdb=" CA ASN E 329 " ideal model delta harmonic sigma weight residual 180.00 -150.28 -29.72 0 5.00e+00 4.00e-02 3.53e+01 ... (remaining 17965 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.976: 4514 0.976 - 1.952: 1 1.952 - 2.928: 0 2.928 - 3.905: 1 3.905 - 4.881: 1 Chirality restraints: 4517 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 0.77 -3.17 2.00e-02 2.50e+03 2.51e+04 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 378 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 2.48 -4.88 2.00e-01 2.50e+01 5.96e+02 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-02 2.50e+03 9.48e+01 ... (remaining 4514 not shown) Planarity restraints: 5083 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1001 " -0.348 2.00e-02 2.50e+03 3.00e-01 1.13e+03 pdb=" C7 NAG A1001 " 0.084 2.00e-02 2.50e+03 pdb=" C8 NAG A1001 " -0.138 2.00e-02 2.50e+03 pdb=" N2 NAG A1001 " 0.534 2.00e-02 2.50e+03 pdb=" O7 NAG A1001 " -0.132 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1001 " -0.323 2.00e-02 2.50e+03 2.80e-01 9.82e+02 pdb=" C7 NAG B1001 " 0.073 2.00e-02 2.50e+03 pdb=" C8 NAG B1001 " -0.133 2.00e-02 2.50e+03 pdb=" N2 NAG B1001 " 0.501 2.00e-02 2.50e+03 pdb=" O7 NAG B1001 " -0.118 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 1 " 0.320 2.00e-02 2.50e+03 2.77e-01 9.60e+02 pdb=" C7 NAG F 1 " -0.071 2.00e-02 2.50e+03 pdb=" C8 NAG F 1 " 0.030 2.00e-02 2.50e+03 pdb=" N2 NAG F 1 " -0.484 2.00e-02 2.50e+03 pdb=" O7 NAG F 1 " 0.204 2.00e-02 2.50e+03 ... (remaining 5080 not shown) Histogram of nonbonded interaction distances: 1.24 - 1.97: 5 1.97 - 2.70: 1916 2.70 - 3.44: 46492 3.44 - 4.17: 69083 4.17 - 4.90: 116153 Nonbonded interactions: 233649 Sorted by model distance: nonbonded pdb=" NH1 ARG C 220 " pdb=" CZ PHE E 102 " model vdw 1.239 3.420 nonbonded pdb=" NH2 ARG C 220 " pdb=" CD1 PHE E 102 " model vdw 1.580 3.420 nonbonded pdb=" NH1 ARG C 220 " pdb=" CE1 PHE E 102 " model vdw 1.598 3.420 nonbonded pdb=" CZ ARG C 220 " pdb=" CE1 PHE E 102 " model vdw 1.652 3.570 nonbonded pdb=" NH2 ARG C 220 " pdb=" CE1 PHE E 102 " model vdw 1.842 3.420 ... (remaining 233644 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 527 or (resid 528 and (name N or name CA or nam \ e C or name O or name CB )) or resid 529 through 663 or (resid 664 and (name N o \ r name CA or name C or name O or name CB )) or resid 665 through 850)) selection = (chain 'B' and (resid 33 through 269 or (resid 270 and (name N or name CA or nam \ e C or name O or name CB )) or resid 271 through 471 or (resid 472 and (name N o \ r name CA or name C or name O or name CB )) or resid 473 through 691 or (resid 6 \ 92 and (name N or name CA or name C or name O or name CB )) or resid 693 through \ 850)) selection = (chain 'C' and (resid 33 through 269 or (resid 270 and (name N or name CA or nam \ e C or name O or name CB )) or resid 271 through 471 or (resid 472 and (name N o \ r name CA or name C or name O or name CB )) or resid 473 through 527 or (resid 5 \ 28 and (name N or name CA or name C or name O or name CB )) or resid 529 through \ 663 or (resid 664 and (name N or name CA or name C or name O or name CB )) or r \ esid 665 through 691 or (resid 692 and (name N or name CA or name C or name O or \ name CB )) or resid 693 through 850)) selection = (chain 'D' and (resid 33 through 269 or (resid 270 and (name N or name CA or nam \ e C or name O or name CB )) or resid 271 through 471 or (resid 472 and (name N o \ r name CA or name C or name O or name CB )) or resid 473 through 527 or (resid 5 \ 28 and (name N or name CA or name C or name O or name CB )) or resid 529 through \ 691 or (resid 692 and (name N or name CA or name C or name O or name CB )) or r \ esid 693 through 850)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 0.720 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: 0.020 Extract box with map and model: 5.270 Check model and map are aligned: 0.420 Set scattering table: 0.250 Process input model: 72.800 Find NCS groups from input model: 2.430 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 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 : 0.008 0.072 29624 Z= 0.557 Angle : 1.088 13.426 40107 Z= 0.644 Chirality : 0.108 4.881 4517 Planarity : 0.012 0.300 5072 Dihedral : 14.054 108.252 11170 Min Nonbonded Distance : 1.239 Molprobity Statistics. All-atom Clashscore : 29.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.51 % Favored : 88.43 % Rotamer: Outliers : 0.19 % Allowed : 1.05 % Favored : 98.76 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.13), residues: 3614 helix: -0.54 (0.13), residues: 1378 sheet: -2.21 (0.26), residues: 386 loop : -2.53 (0.14), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP B 706 HIS 0.012 0.002 HIS B 225 PHE 0.042 0.003 PHE A 42 TYR 0.043 0.003 TYR A 44 ARG 0.014 0.001 ARG B 634 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7228 Ramachandran restraints generated. 3614 Oldfield, 0 Emsley, 3614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7228 Ramachandran restraints generated. 3614 Oldfield, 0 Emsley, 3614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 3158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 180 time to evaluate : 3.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 664 MET cc_start: 0.8573 (tmm) cc_final: 0.8263 (tmm) REVERT: A 691 MET cc_start: 0.8782 (ppp) cc_final: 0.8450 (ppp) REVERT: A 709 MET cc_start: 0.8126 (pmm) cc_final: 0.7882 (pmm) REVERT: A 737 MET cc_start: 0.7995 (ttp) cc_final: 0.7626 (ttp) REVERT: A 793 MET cc_start: 0.9297 (mpp) cc_final: 0.8908 (mpp) REVERT: A 794 MET cc_start: 0.9366 (mpp) cc_final: 0.8744 (mpp) REVERT: B 316 MET cc_start: 0.8260 (mmt) cc_final: 0.8015 (mmt) REVERT: B 705 MET cc_start: 0.9096 (ttt) cc_final: 0.8865 (ttt) REVERT: B 770 MET cc_start: 0.8203 (mmt) cc_final: 0.7692 (mmt) REVERT: C 664 MET cc_start: 0.9080 (ppp) cc_final: 0.8604 (tmm) REVERT: D 534 MET cc_start: 0.9025 (ppp) cc_final: 0.8659 (ppp) REVERT: D 737 MET cc_start: 0.8883 (ptp) cc_final: 0.8509 (ptp) REVERT: E 137 MET cc_start: 0.8403 (mmt) cc_final: 0.8115 (mmp) REVERT: E 308 MET cc_start: 0.8699 (mmp) cc_final: 0.7988 (mmm) outliers start: 6 outliers final: 3 residues processed: 186 average time/residue: 0.3966 time to fit residues: 121.1658 Evaluate side-chains 147 residues out of total 3158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 144 time to evaluate : 4.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 5.9990 chunk 272 optimal weight: 1.9990 chunk 151 optimal weight: 7.9990 chunk 93 optimal weight: 10.0000 chunk 184 optimal weight: 6.9990 chunk 145 optimal weight: 0.1980 chunk 282 optimal weight: 2.9990 chunk 109 optimal weight: 10.0000 chunk 171 optimal weight: 1.9990 chunk 210 optimal weight: 0.8980 chunk 326 optimal weight: 9.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 137 GLN A 604 ASN ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 HIS B 111 HIS ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 HIS B 754 GLN ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 ASN C 610 ASN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 HIS D 591 ASN ** E 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 29624 Z= 0.200 Angle : 0.680 10.978 40107 Z= 0.342 Chirality : 0.045 0.372 4517 Planarity : 0.004 0.046 5072 Dihedral : 8.268 65.358 4317 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 0.16 % Allowed : 5.56 % Favored : 94.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.14), residues: 3614 helix: 0.26 (0.13), residues: 1395 sheet: -1.86 (0.25), residues: 440 loop : -2.15 (0.14), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 706 HIS 0.007 0.001 HIS C 253 PHE 0.046 0.002 PHE E 112 TYR 0.017 0.002 TYR C 44 ARG 0.004 0.000 ARG D 300 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7228 Ramachandran restraints generated. 3614 Oldfield, 0 Emsley, 3614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7228 Ramachandran restraints generated. 3614 Oldfield, 0 Emsley, 3614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 3158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 184 time to evaluate : 3.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 MET cc_start: 0.9253 (ptp) cc_final: 0.9040 (ppp) REVERT: A 534 MET cc_start: 0.7862 (ppp) cc_final: 0.7651 (ppp) REVERT: A 555 PHE cc_start: 0.6450 (m-80) cc_final: 0.6242 (t80) REVERT: A 691 MET cc_start: 0.8730 (ppp) cc_final: 0.8343 (ppp) REVERT: B 360 MET cc_start: 0.8754 (tpp) cc_final: 0.8302 (tpp) REVERT: B 770 MET cc_start: 0.8149 (mmt) cc_final: 0.7613 (mmt) REVERT: B 861 MET cc_start: 0.7834 (mpp) cc_final: 0.7565 (mpp) REVERT: C 97 ASP cc_start: 0.7846 (m-30) cc_final: 0.7586 (m-30) REVERT: C 247 MET cc_start: 0.8240 (tpp) cc_final: 0.8030 (tpp) REVERT: C 276 MET cc_start: 0.8756 (mpp) cc_final: 0.8493 (mpp) REVERT: C 323 MET cc_start: 0.8493 (mmt) cc_final: 0.8223 (tpp) REVERT: C 555 PHE cc_start: 0.8201 (p90) cc_final: 0.7922 (p90) REVERT: C 569 LEU cc_start: 0.9254 (pp) cc_final: 0.8519 (mm) REVERT: C 664 MET cc_start: 0.9075 (ppp) cc_final: 0.8624 (tmm) REVERT: D 248 MET cc_start: 0.8607 (mmm) cc_final: 0.8391 (mmm) REVERT: D 565 MET cc_start: 0.8691 (ppp) cc_final: 0.8420 (ppp) REVERT: D 737 MET cc_start: 0.8696 (ptp) cc_final: 0.8166 (ptm) REVERT: D 770 MET cc_start: 0.7889 (mmm) cc_final: 0.7079 (mmp) REVERT: D 793 MET cc_start: 0.8977 (ppp) cc_final: 0.8729 (ppp) REVERT: D 794 MET cc_start: 0.8620 (ttt) cc_final: 0.8265 (ttt) REVERT: E 308 MET cc_start: 0.8439 (mmp) cc_final: 0.8229 (mmm) outliers start: 5 outliers final: 1 residues processed: 189 average time/residue: 0.3565 time to fit residues: 115.9627 Evaluate side-chains 150 residues out of total 3158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 149 time to evaluate : 3.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 181 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 272 optimal weight: 7.9990 chunk 222 optimal weight: 0.0770 chunk 90 optimal weight: 2.9990 chunk 327 optimal weight: 5.9990 chunk 353 optimal weight: 20.0000 chunk 291 optimal weight: 20.0000 chunk 324 optimal weight: 5.9990 chunk 111 optimal weight: 9.9990 chunk 262 optimal weight: 7.9990 overall best weight: 3.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 178 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 29624 Z= 0.257 Angle : 0.651 11.992 40107 Z= 0.333 Chirality : 0.044 0.361 4517 Planarity : 0.004 0.086 5072 Dihedral : 7.261 55.236 4317 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 17.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 0.03 % Allowed : 4.01 % Favored : 95.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.14), residues: 3614 helix: 0.44 (0.14), residues: 1397 sheet: -1.80 (0.25), residues: 446 loop : -2.06 (0.14), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 296 HIS 0.011 0.001 HIS E 230 PHE 0.026 0.002 PHE E 112 TYR 0.018 0.001 TYR C 44 ARG 0.012 0.000 ARG A 748 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7228 Ramachandran restraints generated. 3614 Oldfield, 0 Emsley, 3614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7228 Ramachandran restraints generated. 3614 Oldfield, 0 Emsley, 3614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 3158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 174 time to evaluate : 3.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 MET cc_start: 0.8078 (ppp) cc_final: 0.7734 (ppp) REVERT: A 691 MET cc_start: 0.8689 (ppp) cc_final: 0.8241 (ppp) REVERT: B 143 ASP cc_start: 0.7160 (OUTLIER) cc_final: 0.6819 (t70) REVERT: B 248 MET cc_start: 0.8309 (tpt) cc_final: 0.7811 (tpt) REVERT: B 323 MET cc_start: 0.8300 (ppp) cc_final: 0.8037 (ppp) REVERT: B 360 MET cc_start: 0.8811 (tpp) cc_final: 0.8443 (tpp) REVERT: B 413 MET cc_start: 0.5108 (ptp) cc_final: 0.4825 (ptp) REVERT: B 565 MET cc_start: 0.8956 (mmm) cc_final: 0.8469 (mmp) REVERT: B 641 TRP cc_start: 0.8174 (m-10) cc_final: 0.7698 (m-10) REVERT: B 709 MET cc_start: 0.8806 (ptp) cc_final: 0.8452 (ptp) REVERT: B 770 MET cc_start: 0.8150 (mmt) cc_final: 0.7624 (mmt) REVERT: C 97 ASP cc_start: 0.7859 (m-30) cc_final: 0.7614 (m-30) REVERT: C 276 MET cc_start: 0.8827 (mpp) cc_final: 0.8510 (mpp) REVERT: C 316 MET cc_start: 0.8409 (mmm) cc_final: 0.8159 (mmm) REVERT: C 565 MET cc_start: 0.8578 (ppp) cc_final: 0.8317 (ppp) REVERT: C 569 LEU cc_start: 0.9221 (pp) cc_final: 0.8648 (pp) REVERT: C 664 MET cc_start: 0.9078 (ppp) cc_final: 0.8686 (tmm) REVERT: C 794 MET cc_start: 0.9169 (pmm) cc_final: 0.8757 (pmm) REVERT: D 565 MET cc_start: 0.8713 (ppp) cc_final: 0.8438 (ppp) REVERT: D 737 MET cc_start: 0.8622 (ptp) cc_final: 0.8155 (ptm) REVERT: D 770 MET cc_start: 0.7753 (mmm) cc_final: 0.6916 (mmp) REVERT: D 793 MET cc_start: 0.8972 (ppp) cc_final: 0.8759 (ppp) REVERT: D 794 MET cc_start: 0.8719 (ttt) cc_final: 0.8317 (ttt) REVERT: E 308 MET cc_start: 0.8462 (mmp) cc_final: 0.7891 (mmm) outliers start: 1 outliers final: 0 residues processed: 175 average time/residue: 0.3570 time to fit residues: 106.4728 Evaluate side-chains 152 residues out of total 3158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 151 time to evaluate : 3.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 323 optimal weight: 8.9990 chunk 246 optimal weight: 6.9990 chunk 169 optimal weight: 9.9990 chunk 36 optimal weight: 30.0000 chunk 156 optimal weight: 20.0000 chunk 219 optimal weight: 2.9990 chunk 328 optimal weight: 10.0000 chunk 347 optimal weight: 5.9990 chunk 171 optimal weight: 7.9990 chunk 311 optimal weight: 7.9990 chunk 93 optimal weight: 0.8980 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 HIS ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 29624 Z= 0.302 Angle : 0.662 8.591 40107 Z= 0.341 Chirality : 0.044 0.404 4517 Planarity : 0.004 0.057 5072 Dihedral : 6.821 59.883 4317 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 18.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 0.03 % Allowed : 3.91 % Favored : 96.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.14), residues: 3614 helix: 0.47 (0.14), residues: 1397 sheet: -1.90 (0.25), residues: 445 loop : -2.06 (0.14), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 296 HIS 0.009 0.002 HIS D 253 PHE 0.047 0.002 PHE D 642 TYR 0.025 0.002 TYR A 44 ARG 0.007 0.001 ARG A 748 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7228 Ramachandran restraints generated. 3614 Oldfield, 0 Emsley, 3614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7228 Ramachandran restraints generated. 3614 Oldfield, 0 Emsley, 3614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 3158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 171 time to evaluate : 3.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 LEU cc_start: 0.9378 (mt) cc_final: 0.9015 (tp) REVERT: A 534 MET cc_start: 0.8098 (ppp) cc_final: 0.7729 (ppp) REVERT: A 620 MET cc_start: 0.8650 (ttm) cc_final: 0.8326 (ttm) REVERT: A 664 MET cc_start: 0.8481 (tmm) cc_final: 0.8273 (tmm) REVERT: A 691 MET cc_start: 0.8760 (ppp) cc_final: 0.8293 (ppp) REVERT: A 709 MET cc_start: 0.8073 (pmm) cc_final: 0.7842 (pmm) REVERT: A 793 MET cc_start: 0.9234 (mpp) cc_final: 0.8927 (mpp) REVERT: A 794 MET cc_start: 0.9363 (mpp) cc_final: 0.8789 (mpp) REVERT: B 565 MET cc_start: 0.8965 (mmm) cc_final: 0.8479 (mmp) REVERT: B 770 MET cc_start: 0.8217 (mmt) cc_final: 0.7730 (mmt) REVERT: C 97 ASP cc_start: 0.7869 (m-30) cc_final: 0.7632 (m-30) REVERT: C 276 MET cc_start: 0.8939 (mpp) cc_final: 0.8661 (mpp) REVERT: C 316 MET cc_start: 0.8587 (mmm) cc_final: 0.8297 (mmm) REVERT: C 565 MET cc_start: 0.8579 (ppp) cc_final: 0.8323 (ppp) REVERT: C 569 LEU cc_start: 0.9350 (pp) cc_final: 0.8782 (pp) REVERT: C 664 MET cc_start: 0.9095 (ppp) cc_final: 0.8775 (tmm) REVERT: C 794 MET cc_start: 0.8996 (pmm) cc_final: 0.8718 (pmm) REVERT: D 534 MET cc_start: 0.9115 (ppp) cc_final: 0.8684 (ppp) REVERT: D 565 MET cc_start: 0.8722 (ppp) cc_final: 0.8436 (ppp) REVERT: D 620 MET cc_start: 0.8624 (mtm) cc_final: 0.8335 (ptp) REVERT: D 737 MET cc_start: 0.8604 (ptp) cc_final: 0.8214 (ptm) REVERT: D 770 MET cc_start: 0.7951 (mmm) cc_final: 0.6702 (mmm) REVERT: D 793 MET cc_start: 0.8995 (ppp) cc_final: 0.8727 (ppp) REVERT: D 794 MET cc_start: 0.8802 (ttt) cc_final: 0.8388 (ttt) REVERT: E 308 MET cc_start: 0.8506 (mmp) cc_final: 0.7993 (mmm) outliers start: 1 outliers final: 1 residues processed: 172 average time/residue: 0.3752 time to fit residues: 110.6570 Evaluate side-chains 154 residues out of total 3158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 153 time to evaluate : 3.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 289 optimal weight: 20.0000 chunk 197 optimal weight: 7.9990 chunk 5 optimal weight: 0.8980 chunk 259 optimal weight: 6.9990 chunk 143 optimal weight: 3.9990 chunk 296 optimal weight: 1.9990 chunk 240 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 177 optimal weight: 6.9990 chunk 312 optimal weight: 8.9990 chunk 87 optimal weight: 20.0000 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 29624 Z= 0.262 Angle : 0.637 9.772 40107 Z= 0.327 Chirality : 0.043 0.348 4517 Planarity : 0.004 0.049 5072 Dihedral : 6.579 59.116 4317 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.14), residues: 3614 helix: 0.60 (0.14), residues: 1396 sheet: -1.78 (0.25), residues: 452 loop : -2.02 (0.14), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 296 HIS 0.007 0.001 HIS D 253 PHE 0.018 0.002 PHE C 555 TYR 0.015 0.001 TYR A 44 ARG 0.006 0.000 ARG A 748 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7228 Ramachandran restraints generated. 3614 Oldfield, 0 Emsley, 3614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7228 Ramachandran restraints generated. 3614 Oldfield, 0 Emsley, 3614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 3158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 3.124 Fit side-chains revert: symmetry clash REVERT: A 50 MET cc_start: 0.7260 (tmm) cc_final: 0.7054 (tmm) REVERT: A 161 LEU cc_start: 0.9339 (mt) cc_final: 0.8933 (tp) REVERT: A 316 MET cc_start: 0.6487 (tmm) cc_final: 0.6210 (tmm) REVERT: A 534 MET cc_start: 0.8019 (ppp) cc_final: 0.7647 (ppp) REVERT: A 620 MET cc_start: 0.8733 (ttm) cc_final: 0.8522 (ttm) REVERT: A 664 MET cc_start: 0.8464 (tmm) cc_final: 0.8161 (tmm) REVERT: A 691 MET cc_start: 0.8725 (ppp) cc_final: 0.8264 (ppp) REVERT: A 793 MET cc_start: 0.9150 (mpp) cc_final: 0.8837 (mpp) REVERT: A 794 MET cc_start: 0.9302 (mpp) cc_final: 0.8703 (mpp) REVERT: B 248 MET cc_start: 0.8314 (tpt) cc_final: 0.7989 (tpp) REVERT: B 360 MET cc_start: 0.8935 (tpp) cc_final: 0.8504 (tpp) REVERT: B 565 MET cc_start: 0.8952 (mmm) cc_final: 0.8455 (mmp) REVERT: B 641 TRP cc_start: 0.7913 (m-10) cc_final: 0.7642 (m-10) REVERT: B 709 MET cc_start: 0.8810 (ptm) cc_final: 0.8542 (ptm) REVERT: B 770 MET cc_start: 0.8227 (mmt) cc_final: 0.7733 (mmt) REVERT: C 97 ASP cc_start: 0.7912 (m-30) cc_final: 0.7676 (m-30) REVERT: C 276 MET cc_start: 0.8952 (mpp) cc_final: 0.8640 (mpp) REVERT: C 555 PHE cc_start: 0.8155 (p90) cc_final: 0.7940 (p90) REVERT: C 565 MET cc_start: 0.8621 (ppp) cc_final: 0.8380 (ppp) REVERT: C 569 LEU cc_start: 0.9359 (pp) cc_final: 0.8566 (mm) REVERT: C 620 MET cc_start: 0.8346 (mmm) cc_final: 0.8140 (mmm) REVERT: C 664 MET cc_start: 0.9020 (ppp) cc_final: 0.8614 (tmm) REVERT: C 794 MET cc_start: 0.9025 (pmm) cc_final: 0.8602 (pmm) REVERT: D 565 MET cc_start: 0.8719 (ppp) cc_final: 0.8418 (ppp) REVERT: D 620 MET cc_start: 0.8525 (mtm) cc_final: 0.8297 (ptp) REVERT: D 737 MET cc_start: 0.8457 (ptp) cc_final: 0.8135 (ptm) REVERT: D 770 MET cc_start: 0.8020 (mmm) cc_final: 0.6739 (mmm) REVERT: D 793 MET cc_start: 0.8961 (ppp) cc_final: 0.8728 (ppp) REVERT: D 794 MET cc_start: 0.8785 (ttt) cc_final: 0.8421 (ttt) REVERT: E 308 MET cc_start: 0.8506 (mmp) cc_final: 0.8003 (mmm) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.3466 time to fit residues: 101.0637 Evaluate side-chains 150 residues out of total 3158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 3.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 117 optimal weight: 8.9990 chunk 313 optimal weight: 6.9990 chunk 68 optimal weight: 8.9990 chunk 204 optimal weight: 0.0980 chunk 85 optimal weight: 2.9990 chunk 348 optimal weight: 0.0040 chunk 289 optimal weight: 20.0000 chunk 161 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 chunk 115 optimal weight: 8.9990 chunk 182 optimal weight: 1.9990 overall best weight: 2.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 HIS ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 754 GLN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29624 Z= 0.190 Angle : 0.598 9.996 40107 Z= 0.303 Chirality : 0.043 0.342 4517 Planarity : 0.004 0.043 5072 Dihedral : 6.259 58.404 4317 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.14), residues: 3614 helix: 0.83 (0.14), residues: 1394 sheet: -1.61 (0.25), residues: 435 loop : -1.92 (0.14), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 296 HIS 0.007 0.001 HIS D 350 PHE 0.021 0.001 PHE D 658 TYR 0.015 0.001 TYR B 764 ARG 0.007 0.000 ARG A 358 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7228 Ramachandran restraints generated. 3614 Oldfield, 0 Emsley, 3614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7228 Ramachandran restraints generated. 3614 Oldfield, 0 Emsley, 3614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 3158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 3.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.7194 (tmm) cc_final: 0.6753 (tmm) REVERT: A 161 LEU cc_start: 0.9287 (mt) cc_final: 0.8908 (tp) REVERT: A 323 MET cc_start: 0.8034 (ppp) cc_final: 0.7652 (ppp) REVERT: A 534 MET cc_start: 0.8087 (ppp) cc_final: 0.7698 (ppp) REVERT: A 620 MET cc_start: 0.8766 (ttm) cc_final: 0.8558 (ttm) REVERT: A 664 MET cc_start: 0.8425 (tmm) cc_final: 0.8079 (tmm) REVERT: A 691 MET cc_start: 0.8758 (ppp) cc_final: 0.8307 (ppp) REVERT: A 709 MET cc_start: 0.7996 (pmm) cc_final: 0.7689 (pmm) REVERT: B 323 MET cc_start: 0.8575 (ptm) cc_final: 0.8103 (ppp) REVERT: B 565 MET cc_start: 0.8947 (mmm) cc_final: 0.8437 (mmp) REVERT: B 641 TRP cc_start: 0.7970 (m-10) cc_final: 0.7620 (m-10) REVERT: B 770 MET cc_start: 0.8260 (mmt) cc_final: 0.7785 (mmt) REVERT: C 97 ASP cc_start: 0.7879 (m-30) cc_final: 0.7645 (m-30) REVERT: C 555 PHE cc_start: 0.8170 (p90) cc_final: 0.7901 (p90) REVERT: C 565 MET cc_start: 0.8598 (ppp) cc_final: 0.8327 (ppp) REVERT: C 569 LEU cc_start: 0.9365 (pp) cc_final: 0.8648 (mm) REVERT: C 620 MET cc_start: 0.8427 (mmm) cc_final: 0.8052 (mmp) REVERT: C 664 MET cc_start: 0.8941 (ppp) cc_final: 0.8516 (tmm) REVERT: C 794 MET cc_start: 0.8844 (pmm) cc_final: 0.8554 (pmm) REVERT: D 565 MET cc_start: 0.8701 (ppp) cc_final: 0.8409 (ppp) REVERT: D 620 MET cc_start: 0.8602 (mtm) cc_final: 0.8251 (ptp) REVERT: D 642 PHE cc_start: 0.8999 (t80) cc_final: 0.8685 (t80) REVERT: D 770 MET cc_start: 0.7757 (mmm) cc_final: 0.7146 (mmm) REVERT: D 793 MET cc_start: 0.8947 (ppp) cc_final: 0.8706 (ppp) REVERT: D 794 MET cc_start: 0.8644 (ttt) cc_final: 0.8234 (ttt) REVERT: E 308 MET cc_start: 0.8453 (mmp) cc_final: 0.7957 (mmm) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.3664 time to fit residues: 109.9641 Evaluate side-chains 153 residues out of total 3158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 3.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 335 optimal weight: 10.0000 chunk 39 optimal weight: 0.0170 chunk 198 optimal weight: 10.0000 chunk 254 optimal weight: 9.9990 chunk 197 optimal weight: 7.9990 chunk 293 optimal weight: 9.9990 chunk 194 optimal weight: 2.9990 chunk 346 optimal weight: 7.9990 chunk 217 optimal weight: 20.0000 chunk 211 optimal weight: 20.0000 chunk 160 optimal weight: 8.9990 overall best weight: 5.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 HIS ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 GLN ** E 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 29624 Z= 0.335 Angle : 0.685 9.242 40107 Z= 0.353 Chirality : 0.044 0.352 4517 Planarity : 0.005 0.053 5072 Dihedral : 6.499 53.619 4317 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 20.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % Rotamer: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.14), residues: 3614 helix: 0.65 (0.14), residues: 1385 sheet: -1.73 (0.24), residues: 478 loop : -1.97 (0.15), residues: 1751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 296 HIS 0.008 0.002 HIS B 225 PHE 0.042 0.002 PHE E 112 TYR 0.021 0.002 TYR C 44 ARG 0.007 0.001 ARG B 300 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7228 Ramachandran restraints generated. 3614 Oldfield, 0 Emsley, 3614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7228 Ramachandran restraints generated. 3614 Oldfield, 0 Emsley, 3614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 3158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 3.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 LEU cc_start: 0.9361 (mt) cc_final: 0.8936 (tp) REVERT: A 316 MET cc_start: 0.6351 (tmm) cc_final: 0.6116 (tmm) REVERT: A 323 MET cc_start: 0.8146 (ppp) cc_final: 0.7841 (ppp) REVERT: A 534 MET cc_start: 0.7980 (ppp) cc_final: 0.7603 (ppp) REVERT: A 664 MET cc_start: 0.8502 (tmm) cc_final: 0.8172 (tmm) REVERT: A 691 MET cc_start: 0.8722 (ppp) cc_final: 0.8246 (ppp) REVERT: A 709 MET cc_start: 0.8133 (pmm) cc_final: 0.7912 (pmm) REVERT: A 793 MET cc_start: 0.9230 (mpp) cc_final: 0.8985 (mpp) REVERT: B 360 MET cc_start: 0.9067 (tpp) cc_final: 0.8722 (tpp) REVERT: B 413 MET cc_start: 0.4815 (ptp) cc_final: 0.4345 (ptp) REVERT: B 565 MET cc_start: 0.8968 (mmm) cc_final: 0.8466 (mmp) REVERT: B 641 TRP cc_start: 0.7961 (m-10) cc_final: 0.7489 (m-10) REVERT: B 770 MET cc_start: 0.8271 (mmt) cc_final: 0.7835 (mmt) REVERT: B 861 MET cc_start: 0.7588 (mpp) cc_final: 0.7326 (mpp) REVERT: C 276 MET cc_start: 0.8921 (mpp) cc_final: 0.8590 (mpp) REVERT: C 555 PHE cc_start: 0.8252 (p90) cc_final: 0.7979 (p90) REVERT: C 569 LEU cc_start: 0.9256 (pp) cc_final: 0.8389 (mt) REVERT: C 620 MET cc_start: 0.8489 (mmm) cc_final: 0.7444 (mmm) REVERT: C 664 MET cc_start: 0.9047 (ppp) cc_final: 0.8648 (tmm) REVERT: C 794 MET cc_start: 0.8827 (pmm) cc_final: 0.8615 (pmm) REVERT: C 861 MET cc_start: 0.0943 (tpp) cc_final: 0.0380 (tpt) REVERT: D 565 MET cc_start: 0.8731 (ppp) cc_final: 0.8431 (ppp) REVERT: D 642 PHE cc_start: 0.8986 (t80) cc_final: 0.8588 (t80) REVERT: D 770 MET cc_start: 0.7844 (mmm) cc_final: 0.7488 (mmm) REVERT: D 793 MET cc_start: 0.9052 (ppp) cc_final: 0.8781 (ppp) REVERT: D 794 MET cc_start: 0.8836 (ttt) cc_final: 0.8462 (ttt) REVERT: E 264 MET cc_start: 0.8205 (mmm) cc_final: 0.7616 (mpp) REVERT: E 308 MET cc_start: 0.8531 (mmp) cc_final: 0.8056 (mmm) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.3700 time to fit residues: 106.9675 Evaluate side-chains 149 residues out of total 3158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 3.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 214 optimal weight: 9.9990 chunk 138 optimal weight: 20.0000 chunk 207 optimal weight: 8.9990 chunk 104 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 67 optimal weight: 8.9990 chunk 220 optimal weight: 7.9990 chunk 236 optimal weight: 7.9990 chunk 171 optimal weight: 4.9990 chunk 32 optimal weight: 9.9990 chunk 272 optimal weight: 4.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 HIS ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 GLN D 784 GLN D 786 GLN ** E 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 29624 Z= 0.355 Angle : 0.706 10.173 40107 Z= 0.365 Chirality : 0.045 0.352 4517 Planarity : 0.004 0.052 5072 Dihedral : 6.617 56.831 4317 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 21.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.14), residues: 3614 helix: 0.50 (0.14), residues: 1378 sheet: -1.78 (0.23), residues: 493 loop : -2.04 (0.14), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 296 HIS 0.017 0.002 HIS E 230 PHE 0.030 0.002 PHE E 112 TYR 0.020 0.002 TYR D 146 ARG 0.006 0.001 ARG A 748 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7228 Ramachandran restraints generated. 3614 Oldfield, 0 Emsley, 3614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7228 Ramachandran restraints generated. 3614 Oldfield, 0 Emsley, 3614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 3158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 3.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 LEU cc_start: 0.9408 (mt) cc_final: 0.8889 (tp) REVERT: A 316 MET cc_start: 0.6371 (tmm) cc_final: 0.6108 (tmm) REVERT: A 534 MET cc_start: 0.7789 (ppp) cc_final: 0.7473 (ppp) REVERT: A 664 MET cc_start: 0.8531 (tmm) cc_final: 0.8158 (tmm) REVERT: A 691 MET cc_start: 0.8509 (ppp) cc_final: 0.8053 (ppp) REVERT: A 709 MET cc_start: 0.8080 (pmm) cc_final: 0.7870 (pmm) REVERT: A 793 MET cc_start: 0.9234 (mpp) cc_final: 0.9030 (mpp) REVERT: B 323 MET cc_start: 0.8154 (ppp) cc_final: 0.7839 (ppp) REVERT: B 360 MET cc_start: 0.9028 (tpp) cc_final: 0.8700 (tpp) REVERT: B 413 MET cc_start: 0.5471 (ptp) cc_final: 0.5257 (ptp) REVERT: B 565 MET cc_start: 0.8983 (mmm) cc_final: 0.8471 (mmp) REVERT: B 576 CYS cc_start: 0.9023 (t) cc_final: 0.8735 (p) REVERT: B 641 TRP cc_start: 0.7959 (m-10) cc_final: 0.7295 (m-10) REVERT: B 709 MET cc_start: 0.8936 (ptp) cc_final: 0.8594 (ptm) REVERT: B 770 MET cc_start: 0.8252 (mmt) cc_final: 0.7834 (mmt) REVERT: B 861 MET cc_start: 0.7663 (mpp) cc_final: 0.7399 (mpp) REVERT: C 276 MET cc_start: 0.8988 (mpp) cc_final: 0.8715 (mpp) REVERT: C 298 MET cc_start: 0.8989 (mtm) cc_final: 0.8787 (mtm) REVERT: C 565 MET cc_start: 0.8635 (ppp) cc_final: 0.8418 (ppp) REVERT: C 569 LEU cc_start: 0.9302 (pp) cc_final: 0.8540 (mt) REVERT: C 620 MET cc_start: 0.8540 (mmm) cc_final: 0.8011 (mmp) REVERT: C 664 MET cc_start: 0.9108 (ppp) cc_final: 0.8711 (tmm) REVERT: C 794 MET cc_start: 0.8870 (pmm) cc_final: 0.8616 (pmm) REVERT: C 861 MET cc_start: 0.0898 (tpp) cc_final: 0.0342 (tpt) REVERT: D 360 MET cc_start: 0.8393 (tpp) cc_final: 0.8132 (tpp) REVERT: D 770 MET cc_start: 0.7921 (mmm) cc_final: 0.7629 (mmm) REVERT: D 793 MET cc_start: 0.9016 (ppp) cc_final: 0.8788 (ppp) REVERT: D 794 MET cc_start: 0.8897 (ttt) cc_final: 0.8512 (ttt) REVERT: E 308 MET cc_start: 0.8558 (mmp) cc_final: 0.8051 (mmm) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.3613 time to fit residues: 104.1601 Evaluate side-chains 148 residues out of total 3158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 3.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 315 optimal weight: 4.9990 chunk 332 optimal weight: 5.9990 chunk 303 optimal weight: 0.9990 chunk 323 optimal weight: 0.0010 chunk 194 optimal weight: 6.9990 chunk 140 optimal weight: 40.0000 chunk 253 optimal weight: 8.9990 chunk 99 optimal weight: 7.9990 chunk 292 optimal weight: 4.9990 chunk 305 optimal weight: 10.0000 chunk 322 optimal weight: 7.9990 overall best weight: 3.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 HIS ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 29624 Z= 0.232 Angle : 0.634 11.404 40107 Z= 0.324 Chirality : 0.043 0.345 4517 Planarity : 0.004 0.044 5072 Dihedral : 6.327 58.671 4317 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.14), residues: 3614 helix: 0.76 (0.14), residues: 1384 sheet: -1.63 (0.23), residues: 502 loop : -1.96 (0.15), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 296 HIS 0.007 0.001 HIS D 253 PHE 0.023 0.002 PHE D 658 TYR 0.037 0.001 TYR A 44 ARG 0.004 0.000 ARG A 748 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7228 Ramachandran restraints generated. 3614 Oldfield, 0 Emsley, 3614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7228 Ramachandran restraints generated. 3614 Oldfield, 0 Emsley, 3614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 3158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 3.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 LEU cc_start: 0.9343 (mt) cc_final: 0.8928 (tp) REVERT: A 323 MET cc_start: 0.8231 (ppp) cc_final: 0.7719 (ppp) REVERT: A 534 MET cc_start: 0.7822 (ppp) cc_final: 0.7474 (ppp) REVERT: A 620 MET cc_start: 0.8621 (ttm) cc_final: 0.8382 (ttm) REVERT: A 664 MET cc_start: 0.8450 (tmm) cc_final: 0.8159 (tmm) REVERT: A 691 MET cc_start: 0.8472 (ppp) cc_final: 0.8004 (ppp) REVERT: A 709 MET cc_start: 0.7993 (pmm) cc_final: 0.7770 (pmm) REVERT: B 248 MET cc_start: 0.8243 (tpt) cc_final: 0.7826 (tpt) REVERT: B 323 MET cc_start: 0.8233 (ppp) cc_final: 0.7927 (ppp) REVERT: B 360 MET cc_start: 0.8981 (tpp) cc_final: 0.8616 (tpp) REVERT: B 501 MET cc_start: 0.8541 (mtt) cc_final: 0.8334 (tmm) REVERT: B 565 MET cc_start: 0.8973 (mmm) cc_final: 0.8409 (mmp) REVERT: B 576 CYS cc_start: 0.8917 (t) cc_final: 0.8625 (p) REVERT: B 641 TRP cc_start: 0.7952 (m-10) cc_final: 0.7490 (m-10) REVERT: B 705 MET cc_start: 0.9053 (ttt) cc_final: 0.8741 (ttt) REVERT: B 709 MET cc_start: 0.8878 (ptp) cc_final: 0.8541 (ptm) REVERT: B 737 MET cc_start: 0.8435 (ppp) cc_final: 0.8012 (ppp) REVERT: B 770 MET cc_start: 0.8226 (mmt) cc_final: 0.7782 (mmt) REVERT: C 276 MET cc_start: 0.9058 (mpp) cc_final: 0.8794 (mpp) REVERT: C 569 LEU cc_start: 0.9287 (pp) cc_final: 0.8558 (mt) REVERT: C 620 MET cc_start: 0.8659 (mmm) cc_final: 0.7757 (mmm) REVERT: C 664 MET cc_start: 0.8995 (ppp) cc_final: 0.8590 (tmm) REVERT: C 794 MET cc_start: 0.8798 (pmm) cc_final: 0.8508 (pmm) REVERT: D 642 PHE cc_start: 0.8972 (t80) cc_final: 0.8551 (t80) REVERT: D 737 MET cc_start: 0.8636 (ptp) cc_final: 0.8178 (ptm) REVERT: D 770 MET cc_start: 0.7920 (mmm) cc_final: 0.7620 (mmm) REVERT: E 308 MET cc_start: 0.8515 (mmp) cc_final: 0.8033 (mmm) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.3436 time to fit residues: 100.8848 Evaluate side-chains 149 residues out of total 3158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 3.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 212 optimal weight: 1.9990 chunk 341 optimal weight: 5.9990 chunk 208 optimal weight: 50.0000 chunk 162 optimal weight: 0.7980 chunk 237 optimal weight: 8.9990 chunk 358 optimal weight: 5.9990 chunk 330 optimal weight: 5.9990 chunk 285 optimal weight: 0.0470 chunk 29 optimal weight: 8.9990 chunk 220 optimal weight: 10.0000 chunk 175 optimal weight: 0.3980 overall best weight: 1.8482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 178 GLN ** E 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29624 Z= 0.179 Angle : 0.608 10.609 40107 Z= 0.307 Chirality : 0.043 0.352 4517 Planarity : 0.004 0.043 5072 Dihedral : 5.966 57.544 4317 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.59 % Favored : 93.39 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.14), residues: 3614 helix: 0.96 (0.14), residues: 1384 sheet: -1.47 (0.24), residues: 506 loop : -1.84 (0.15), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP C 640 HIS 0.005 0.001 HIS D 253 PHE 0.022 0.001 PHE D 658 TYR 0.023 0.001 TYR B 566 ARG 0.004 0.000 ARG B 748 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7228 Ramachandran restraints generated. 3614 Oldfield, 0 Emsley, 3614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7228 Ramachandran restraints generated. 3614 Oldfield, 0 Emsley, 3614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 3158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 3.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 LEU cc_start: 0.9322 (mt) cc_final: 0.8907 (tp) REVERT: A 276 MET cc_start: 0.7969 (mmm) cc_final: 0.7694 (mmm) REVERT: A 323 MET cc_start: 0.8173 (ppp) cc_final: 0.7660 (ppp) REVERT: A 534 MET cc_start: 0.7936 (ppp) cc_final: 0.7465 (ppp) REVERT: A 664 MET cc_start: 0.8381 (tmm) cc_final: 0.8103 (tmm) REVERT: A 691 MET cc_start: 0.8562 (ppp) cc_final: 0.8165 (ppp) REVERT: A 709 MET cc_start: 0.7992 (pmm) cc_final: 0.7401 (mmm) REVERT: A 793 MET cc_start: 0.9139 (mpp) cc_final: 0.8793 (mpp) REVERT: B 360 MET cc_start: 0.8970 (tpp) cc_final: 0.8501 (tpp) REVERT: B 413 MET cc_start: 0.4867 (ptp) cc_final: 0.4505 (ptp) REVERT: B 565 MET cc_start: 0.8937 (mmm) cc_final: 0.8400 (mmp) REVERT: B 641 TRP cc_start: 0.7892 (m-10) cc_final: 0.7595 (m-10) REVERT: B 705 MET cc_start: 0.9043 (ttt) cc_final: 0.8750 (ttt) REVERT: B 709 MET cc_start: 0.8908 (ptp) cc_final: 0.8653 (ptm) REVERT: B 770 MET cc_start: 0.8246 (mmt) cc_final: 0.7775 (mmt) REVERT: C 276 MET cc_start: 0.9026 (mpp) cc_final: 0.8774 (mpp) REVERT: C 565 MET cc_start: 0.8645 (ppp) cc_final: 0.8368 (ppp) REVERT: C 569 LEU cc_start: 0.9242 (pp) cc_final: 0.8474 (mm) REVERT: C 620 MET cc_start: 0.8655 (mmm) cc_final: 0.7830 (mmm) REVERT: C 664 MET cc_start: 0.8912 (ppp) cc_final: 0.8430 (tmm) REVERT: C 794 MET cc_start: 0.8800 (pmm) cc_final: 0.8501 (pmm) REVERT: D 360 MET cc_start: 0.8235 (tpp) cc_final: 0.7891 (tpp) REVERT: D 705 MET cc_start: 0.9324 (ptp) cc_final: 0.8785 (pmm) REVERT: D 737 MET cc_start: 0.8554 (ptp) cc_final: 0.8150 (ptm) REVERT: D 770 MET cc_start: 0.7926 (mmm) cc_final: 0.7540 (mmm) REVERT: D 794 MET cc_start: 0.8669 (ttt) cc_final: 0.8272 (ttt) REVERT: E 264 MET cc_start: 0.8154 (mmm) cc_final: 0.7764 (mmm) REVERT: E 308 MET cc_start: 0.8526 (mmp) cc_final: 0.8118 (mmm) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.3576 time to fit residues: 103.1722 Evaluate side-chains 146 residues out of total 3158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 3.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 226 optimal weight: 0.8980 chunk 304 optimal weight: 40.0000 chunk 87 optimal weight: 7.9990 chunk 263 optimal weight: 0.9990 chunk 42 optimal weight: 20.0000 chunk 79 optimal weight: 10.0000 chunk 286 optimal weight: 8.9990 chunk 119 optimal weight: 0.0670 chunk 293 optimal weight: 4.9990 chunk 36 optimal weight: 30.0000 chunk 52 optimal weight: 5.9990 overall best weight: 2.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 GLN ** E 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.061347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.047730 restraints weight = 225942.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.048253 restraints weight = 136748.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.048299 restraints weight = 124733.667| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29624 Z= 0.199 Angle : 0.610 11.411 40107 Z= 0.308 Chirality : 0.042 0.350 4517 Planarity : 0.004 0.043 5072 Dihedral : 5.860 58.722 4317 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.95 % Favored : 93.03 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.14), residues: 3614 helix: 1.07 (0.14), residues: 1383 sheet: -1.43 (0.24), residues: 506 loop : -1.80 (0.15), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 296 HIS 0.006 0.001 HIS D 253 PHE 0.023 0.001 PHE D 555 TYR 0.021 0.001 TYR B 566 ARG 0.004 0.000 ARG D 300 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4166.72 seconds wall clock time: 79 minutes 3.14 seconds (4743.14 seconds total)