Starting phenix.real_space_refine on Fri Feb 16 16:32:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x6c_22075/02_2024/6x6c_22075_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x6c_22075/02_2024/6x6c_22075.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x6c_22075/02_2024/6x6c_22075_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x6c_22075/02_2024/6x6c_22075_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x6c_22075/02_2024/6x6c_22075_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x6c_22075/02_2024/6x6c_22075.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x6c_22075/02_2024/6x6c_22075.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x6c_22075/02_2024/6x6c_22075_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x6c_22075/02_2024/6x6c_22075_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 71 5.16 5 B 2 2.79 5 C 10190 2.51 5 N 2694 2.21 5 O 2878 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 19": "OD1" <-> "OD2" Residue "A PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 143": "OD1" <-> "OD2" Residue "A PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 235": "OD1" <-> "OD2" Residue "A ASP 251": "OD1" <-> "OD2" Residue "A TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 321": "OE1" <-> "OE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 359": "NH1" <-> "NH2" Residue "A PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 393": "OE1" <-> "OE2" Residue "A GLU 415": "OE1" <-> "OE2" Residue "A TYR 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 437": "OD1" <-> "OD2" Residue "A GLU 470": "OE1" <-> "OE2" Residue "A PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 486": "OE1" <-> "OE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 537": "OE1" <-> "OE2" Residue "A PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 597": "OE1" <-> "OE2" Residue "A ASP 604": "OD1" <-> "OD2" Residue "A TYR 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 672": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 703": "OE1" <-> "OE2" Residue "A ASP 704": "OD1" <-> "OD2" Residue "A GLU 707": "OE1" <-> "OE2" Residue "A GLU 714": "OE1" <-> "OE2" Residue "A TYR 731": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 830": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 838": "OE1" <-> "OE2" Residue "A GLU 846": "OE1" <-> "OE2" Residue "A PHE 858": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 110": "OD1" <-> "OD2" Residue "D TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 235": "OD1" <-> "OD2" Residue "D GLU 248": "OE1" <-> "OE2" Residue "D GLU 249": "OE1" <-> "OE2" Residue "D GLU 278": "OE1" <-> "OE2" Residue "D GLU 286": "OE1" <-> "OE2" Residue "D GLU 335": "OE1" <-> "OE2" Residue "D PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 359": "NH1" <-> "NH2" Residue "D TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 370": "OD1" <-> "OD2" Residue "D PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 446": "OE1" <-> "OE2" Residue "D ASP 477": "OD1" <-> "OD2" Residue "D PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 520": "OD1" <-> "OD2" Residue "D TYR 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 557": "OD1" <-> "OD2" Residue "D PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 618": "OD1" <-> "OD2" Residue "D PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 672": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 731": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 809": "OE1" <-> "OE2" Residue "D TYR 830": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 838": "OE1" <-> "OE2" Residue "D GLU 846": "OE1" <-> "OE2" Residue "D PHE 858": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 1267": "OE1" <-> "OE2" Residue "F ARG 1274": "NH1" <-> "NH2" Residue "F GLU 1306": "OE1" <-> "OE2" Residue "F GLU 1308": "OE1" <-> "OE2" Residue "F ASP 1317": "OD1" <-> "OD2" Residue "F TYR 1324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 1347": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15835 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 846, 6816 Classifications: {'peptide': 846} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 54, 'TRANS': 791} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 6816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 846, 6816 Classifications: {'peptide': 846} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 54, 'TRANS': 791} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1068 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 10, 'TRANS': 123} Chain: "F" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1105 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 127} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'GK2': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'GK2': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.55, per 1000 atoms: 0.54 Number of scatterers: 15835 At special positions: 0 Unit cell: (127.05, 143.55, 97.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 71 16.00 O 2878 8.00 N 2694 7.00 C 10190 6.00 B 2 5.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.44 Conformation dependent library (CDL) restraints added in 2.9 seconds 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3656 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 42 helices and 30 sheets defined 17.0% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.59 Creating SS restraints... Processing helix chain 'A' and resid 31 through 42 removed outlier: 3.572A pdb=" N ARG A 42 " --> pdb=" O ILE A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 48 No H-bonds generated for 'chain 'A' and resid 45 through 48' Processing helix chain 'A' and resid 117 through 119 No H-bonds generated for 'chain 'A' and resid 117 through 119' Processing helix chain 'A' and resid 123 through 131 Processing helix chain 'A' and resid 244 through 248 Processing helix chain 'A' and resid 282 through 284 No H-bonds generated for 'chain 'A' and resid 282 through 284' Processing helix chain 'A' and resid 295 through 297 No H-bonds generated for 'chain 'A' and resid 295 through 297' Processing helix chain 'A' and resid 342 through 345 No H-bonds generated for 'chain 'A' and resid 342 through 345' Processing helix chain 'A' and resid 383 through 385 No H-bonds generated for 'chain 'A' and resid 383 through 385' Processing helix chain 'A' and resid 393 through 402 Processing helix chain 'A' and resid 584 through 586 No H-bonds generated for 'chain 'A' and resid 584 through 586' Processing helix chain 'A' and resid 662 through 670 Processing helix chain 'A' and resid 687 through 693 removed outlier: 3.626A pdb=" N ALA A 692 " --> pdb=" O ARG A 688 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LEU A 693 " --> pdb=" O PHE A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 715 Processing helix chain 'A' and resid 730 through 742 removed outlier: 3.818A pdb=" N HIS A 742 " --> pdb=" O GLY A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 761 No H-bonds generated for 'chain 'A' and resid 759 through 761' Processing helix chain 'A' and resid 764 through 771 removed outlier: 4.069A pdb=" N ARG A 769 " --> pdb=" O GLY A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 783 Processing helix chain 'A' and resid 786 through 792 removed outlier: 3.679A pdb=" N VAL A 790 " --> pdb=" O ALA A 787 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N GLU A 791 " --> pdb=" O LEU A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 826 Processing helix chain 'A' and resid 845 through 862 Processing helix chain 'D' and resid 31 through 48 removed outlier: 3.664A pdb=" N ARG D 42 " --> pdb=" O ILE D 38 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS D 43 " --> pdb=" O HIS D 39 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N TYR D 44 " --> pdb=" O GLY D 40 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N SER D 45 " --> pdb=" O SER D 41 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLY D 46 " --> pdb=" O ARG D 42 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N LEU D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 119 No H-bonds generated for 'chain 'D' and resid 117 through 119' Processing helix chain 'D' and resid 123 through 132 removed outlier: 3.651A pdb=" N LEU D 127 " --> pdb=" O ARG D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 249 Processing helix chain 'D' and resid 295 through 297 No H-bonds generated for 'chain 'D' and resid 295 through 297' Processing helix chain 'D' and resid 342 through 345 No H-bonds generated for 'chain 'D' and resid 342 through 345' Processing helix chain 'D' and resid 383 through 385 No H-bonds generated for 'chain 'D' and resid 383 through 385' Processing helix chain 'D' and resid 393 through 402 Processing helix chain 'D' and resid 584 through 586 No H-bonds generated for 'chain 'D' and resid 584 through 586' Processing helix chain 'D' and resid 662 through 670 Processing helix chain 'D' and resid 687 through 693 removed outlier: 3.643A pdb=" N ALA D 692 " --> pdb=" O ARG D 688 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N LEU D 693 " --> pdb=" O PHE D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 701 through 715 Processing helix chain 'D' and resid 730 through 742 removed outlier: 3.824A pdb=" N HIS D 742 " --> pdb=" O GLY D 739 " (cutoff:3.500A) Processing helix chain 'D' and resid 764 through 770 removed outlier: 4.100A pdb=" N ARG D 769 " --> pdb=" O GLY D 765 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR D 770 " --> pdb=" O TYR D 766 " (cutoff:3.500A) Processing helix chain 'D' and resid 778 through 783 Processing helix chain 'D' and resid 786 through 788 No H-bonds generated for 'chain 'D' and resid 786 through 788' Processing helix chain 'D' and resid 790 through 792 No H-bonds generated for 'chain 'D' and resid 790 through 792' Processing helix chain 'D' and resid 813 through 826 Processing helix chain 'D' and resid 845 through 862 Processing helix chain 'E' and resid 1132 through 1138 removed outlier: 3.608A pdb=" N GLU E1138 " --> pdb=" O GLN E1134 " (cutoff:3.500A) Processing helix chain 'F' and resid 1257 through 1269 Processing sheet with id= A, first strand: chain 'A' and resid 57 through 60 removed outlier: 6.702A pdb=" N ILE A 91 " --> pdb=" O SER A 69 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ARG A 71 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N SER A 89 " --> pdb=" O ARG A 71 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N TYR A 73 " --> pdb=" O LEU A 87 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU A 87 " --> pdb=" O TYR A 73 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LEU A 75 " --> pdb=" O SER A 85 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N SER A 85 " --> pdb=" O LEU A 75 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 142 through 145 removed outlier: 4.529A pdb=" N LEU A 159 " --> pdb=" O ILE A 180 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 200 through 205 Processing sheet with id= D, first strand: chain 'A' and resid 237 through 239 removed outlier: 3.503A pdb=" N PHE A 322 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 8.882A pdb=" N LEU A 317 " --> pdb=" O LEU A 338 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LEU A 338 " --> pdb=" O LEU A 317 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 256 through 258 Processing sheet with id= F, first strand: chain 'A' and resid 287 through 291 Processing sheet with id= G, first strand: chain 'A' and resid 351 through 357 removed outlier: 6.718A pdb=" N MET A 367 " --> pdb=" O ALA A 353 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ALA A 355 " --> pdb=" O TRP A 365 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N TRP A 365 " --> pdb=" O ALA A 355 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N TRP A 357 " --> pdb=" O TYR A 363 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N TYR A 363 " --> pdb=" O TRP A 357 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TYR A 413 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LEU A 380 " --> pdb=" O VAL A 411 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N VAL A 411 " --> pdb=" O LEU A 380 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 440 through 445 removed outlier: 3.504A pdb=" N HIS A 453 " --> pdb=" O ASN A 445 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 505 through 507 Processing sheet with id= J, first strand: chain 'A' and resid 547 through 552 Processing sheet with id= K, first strand: chain 'A' and resid 609 through 614 removed outlier: 4.425A pdb=" N ILE A 677 " --> pdb=" O PHE A 642 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL A 749 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 8.873A pdb=" N GLY A 728 " --> pdb=" O VAL A 749 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE A 751 " --> pdb=" O GLY A 728 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLN A 831 " --> pdb=" O ILE A 802 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N HIS A 804 " --> pdb=" O GLN A 831 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLN A 833 " --> pdb=" O HIS A 804 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 572 through 574 removed outlier: 6.036A pdb=" N VAL A 574 " --> pdb=" O SER A 594 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N SER A 594 " --> pdb=" O VAL A 574 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 57 through 60 removed outlier: 6.706A pdb=" N ILE D 91 " --> pdb=" O SER D 69 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ARG D 71 " --> pdb=" O SER D 89 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N SER D 89 " --> pdb=" O ARG D 71 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N TYR D 73 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU D 87 " --> pdb=" O TYR D 73 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N LEU D 75 " --> pdb=" O SER D 85 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N SER D 85 " --> pdb=" O LEU D 75 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 142 through 145 removed outlier: 4.531A pdb=" N LEU D 159 " --> pdb=" O ILE D 180 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 200 through 205 Processing sheet with id= P, first strand: chain 'D' and resid 237 through 239 removed outlier: 3.527A pdb=" N VAL D 280 " --> pdb=" O SER D 238 " (cutoff:3.500A) removed outlier: 8.958A pdb=" N LEU D 317 " --> pdb=" O LEU D 338 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N LEU D 338 " --> pdb=" O LEU D 317 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 256 through 258 Processing sheet with id= R, first strand: chain 'D' and resid 271 through 273 removed outlier: 3.511A pdb=" N PHE D 322 " --> pdb=" O LEU D 273 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 287 through 291 Processing sheet with id= T, first strand: chain 'D' and resid 351 through 357 removed outlier: 6.645A pdb=" N MET D 367 " --> pdb=" O ALA D 353 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ALA D 355 " --> pdb=" O TRP D 365 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TRP D 365 " --> pdb=" O ALA D 355 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N TRP D 357 " --> pdb=" O TYR D 363 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N TYR D 363 " --> pdb=" O TRP D 357 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR D 413 " --> pdb=" O LEU D 378 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N LEU D 380 " --> pdb=" O VAL D 411 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N VAL D 411 " --> pdb=" O LEU D 380 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 427 through 429 Processing sheet with id= V, first strand: chain 'D' and resid 505 through 507 Processing sheet with id= W, first strand: chain 'D' and resid 547 through 552 Processing sheet with id= X, first strand: chain 'D' and resid 609 through 614 removed outlier: 4.358A pdb=" N ILE D 677 " --> pdb=" O PHE D 642 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N TRP D 729 " --> pdb=" O VAL D 643 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL D 749 " --> pdb=" O ILE D 726 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N GLY D 728 " --> pdb=" O VAL D 749 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE D 751 " --> pdb=" O GLY D 728 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLN D 831 " --> pdb=" O ILE D 802 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N HIS D 804 " --> pdb=" O GLN D 831 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N GLN D 833 " --> pdb=" O HIS D 804 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 572 through 574 removed outlier: 6.364A pdb=" N VAL D 574 " --> pdb=" O SER D 594 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N SER D 594 " --> pdb=" O VAL D 574 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 1152 through 1155 removed outlier: 4.146A pdb=" N VAL E1123 " --> pdb=" O PHE E1102 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE E1102 " --> pdb=" O VAL E1123 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU E1097 " --> pdb=" O ASP E1092 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ASP E1092 " --> pdb=" O LEU E1097 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N ARG E1099 " --> pdb=" O VAL E1090 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N VAL E1090 " --> pdb=" O ARG E1099 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 1116 through 1118 Processing sheet with id= AB, first strand: chain 'E' and resid 1184 through 1188 Processing sheet with id= AC, first strand: chain 'F' and resid 1234 through 1236 removed outlier: 3.975A pdb=" N ILE F1253 " --> pdb=" O VAL F1234 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 1306 through 1308 removed outlier: 3.654A pdb=" N LEU F1334 " --> pdb=" O ALA F1348 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ALA F1348 " --> pdb=" O LEU F1334 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL F1336 " --> pdb=" O TRP F1346 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N TRP F1346 " --> pdb=" O VAL F1336 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ASP F1338 " --> pdb=" O LEU F1344 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N LEU F1344 " --> pdb=" O ASP F1338 " (cutoff:3.500A) 429 hydrogen bonds defined for protein. 1113 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: 6.34 Time building geometry restraints manager: 6.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2574 1.31 - 1.43: 4653 1.43 - 1.56: 8967 1.56 - 1.69: 9 1.69 - 1.81: 109 Bond restraints: 16312 Sorted by residual: bond pdb=" B15 GK2 A 901 " pdb=" O16 GK2 A 901 " ideal model delta sigma weight residual 1.338 1.534 -0.196 2.00e-02 2.50e+03 9.65e+01 bond pdb=" B15 GK2 D 901 " pdb=" O16 GK2 D 901 " ideal model delta sigma weight residual 1.338 1.534 -0.196 2.00e-02 2.50e+03 9.58e+01 bond pdb=" C2 GK2 D 901 " pdb=" C3 GK2 D 901 " ideal model delta sigma weight residual 1.338 1.517 -0.179 2.00e-02 2.50e+03 7.99e+01 bond pdb=" C2 GK2 A 901 " pdb=" C3 GK2 A 901 " ideal model delta sigma weight residual 1.338 1.515 -0.177 2.00e-02 2.50e+03 7.80e+01 bond pdb=" B15 GK2 D 901 " pdb=" O17 GK2 D 901 " ideal model delta sigma weight residual 1.364 1.536 -0.172 2.00e-02 2.50e+03 7.41e+01 ... (remaining 16307 not shown) Histogram of bond angle deviations from ideal: 95.78 - 103.70: 297 103.70 - 111.62: 6616 111.62 - 119.55: 6843 119.55 - 127.47: 8142 127.47 - 135.39: 254 Bond angle restraints: 22152 Sorted by residual: angle pdb=" N SER D 146 " pdb=" CA SER D 146 " pdb=" C SER D 146 " ideal model delta sigma weight residual 111.28 122.28 -11.00 1.09e+00 8.42e-01 1.02e+02 angle pdb=" N LEU D 229 " pdb=" CA LEU D 229 " pdb=" C LEU D 229 " ideal model delta sigma weight residual 111.28 120.27 -8.99 1.09e+00 8.42e-01 6.80e+01 angle pdb=" N ASP D 772 " pdb=" CA ASP D 772 " pdb=" C ASP D 772 " ideal model delta sigma weight residual 110.97 118.45 -7.48 1.09e+00 8.42e-01 4.71e+01 angle pdb=" N VAL D 811 " pdb=" CA VAL D 811 " pdb=" C VAL D 811 " ideal model delta sigma weight residual 107.51 98.12 9.39 1.49e+00 4.50e-01 3.97e+01 angle pdb=" C ALA A 52 " pdb=" N PRO A 53 " pdb=" CA PRO A 53 " ideal model delta sigma weight residual 119.90 126.20 -6.30 1.02e+00 9.61e-01 3.82e+01 ... (remaining 22147 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.11: 8763 18.11 - 36.23: 717 36.23 - 54.34: 96 54.34 - 72.45: 44 72.45 - 90.56: 10 Dihedral angle restraints: 9630 sinusoidal: 3928 harmonic: 5702 Sorted by residual: dihedral pdb=" CA GLY A 435 " pdb=" C GLY A 435 " pdb=" N GLU A 436 " pdb=" CA GLU A 436 " ideal model delta harmonic sigma weight residual -180.00 -153.21 -26.79 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" CA ASP D 235 " pdb=" C ASP D 235 " pdb=" N PRO D 236 " pdb=" CA PRO D 236 " ideal model delta harmonic sigma weight residual -180.00 -153.34 -26.66 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" CA GLU A 436 " pdb=" C GLU A 436 " pdb=" N ASP A 437 " pdb=" CA ASP A 437 " ideal model delta harmonic sigma weight residual 180.00 153.36 26.64 0 5.00e+00 4.00e-02 2.84e+01 ... (remaining 9627 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 1810 0.090 - 0.180: 432 0.180 - 0.269: 68 0.269 - 0.359: 11 0.359 - 0.449: 4 Chirality restraints: 2325 Sorted by residual: chirality pdb=" CA SER D 146 " pdb=" N SER D 146 " pdb=" C SER D 146 " pdb=" CB SER D 146 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.04e+00 chirality pdb=" CB ILE A 726 " pdb=" CA ILE A 726 " pdb=" CG1 ILE A 726 " pdb=" CG2 ILE A 726 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.42 2.00e-01 2.50e+01 4.34e+00 chirality pdb=" CG LEU D 103 " pdb=" CB LEU D 103 " pdb=" CD1 LEU D 103 " pdb=" CD2 LEU D 103 " both_signs ideal model delta sigma weight residual False -2.59 -2.18 -0.41 2.00e-01 2.50e+01 4.12e+00 ... (remaining 2322 not shown) Planarity restraints: 2872 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 173 " -0.092 5.00e-02 4.00e+02 1.41e-01 3.20e+01 pdb=" N PRO D 174 " 0.245 5.00e-02 4.00e+02 pdb=" CA PRO D 174 " -0.078 5.00e-02 4.00e+02 pdb=" CD PRO D 174 " -0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 726 " 0.024 2.00e-02 2.50e+03 4.80e-02 2.30e+01 pdb=" C ILE D 726 " -0.083 2.00e-02 2.50e+03 pdb=" O ILE D 726 " 0.031 2.00e-02 2.50e+03 pdb=" N HIS D 727 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 247 " -0.020 2.00e-02 2.50e+03 4.05e-02 1.64e+01 pdb=" C GLN A 247 " 0.070 2.00e-02 2.50e+03 pdb=" O GLN A 247 " -0.027 2.00e-02 2.50e+03 pdb=" N GLU A 248 " -0.024 2.00e-02 2.50e+03 ... (remaining 2869 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 323 2.66 - 3.22: 14024 3.22 - 3.78: 26323 3.78 - 4.34: 36254 4.34 - 4.90: 58891 Nonbonded interactions: 135815 Sorted by model distance: nonbonded pdb=" N GLU A 809 " pdb=" OE1 GLU A 809 " model vdw 2.098 2.520 nonbonded pdb=" OH TYR A 466 " pdb=" OE2 GLU A 478 " model vdw 2.211 2.440 nonbonded pdb=" O ALA D 713 " pdb=" O TYR D 716 " model vdw 2.226 3.040 nonbonded pdb=" NE ARG A 131 " pdb=" OE1 GLU A 248 " model vdw 2.250 2.520 nonbonded pdb=" O TYR F1285 " pdb=" OH TYR F1290 " model vdw 2.258 2.440 ... (remaining 135810 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' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.190 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: 13.390 Check model and map are aligned: 0.220 Set scattering table: 0.150 Process input model: 45.620 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 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 : 0.010 0.196 16312 Z= 0.646 Angle : 1.370 15.212 22152 Z= 0.786 Chirality : 0.081 0.449 2325 Planarity : 0.010 0.141 2872 Dihedral : 13.922 90.562 5974 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.49 % Favored : 93.40 % Rotamer: Outliers : 0.58 % Allowed : 1.05 % Favored : 98.37 % 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: -2.84 (0.17), residues: 1956 helix: -1.04 (0.27), residues: 287 sheet: -2.42 (0.18), residues: 548 loop : -1.81 (0.17), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.004 TRP E1132 HIS 0.020 0.003 HIS F1223 PHE 0.038 0.004 PHE D 201 TYR 0.043 0.004 TYR D 781 ARG 0.031 0.002 ARG D 359 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 196 time to evaluate : 1.908 Fit side-chains revert: symmetry clash REVERT: A 256 TYR cc_start: 0.8719 (p90) cc_final: 0.8407 (p90) REVERT: A 624 MET cc_start: 0.8248 (mtm) cc_final: 0.7945 (mtp) REVERT: A 771 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.8201 (mmm) REVERT: D 107 GLN cc_start: 0.7942 (mm110) cc_final: 0.7527 (mp10) REVERT: D 175 MET cc_start: 0.6550 (ppp) cc_final: 0.6255 (tmm) REVERT: D 229 LEU cc_start: 0.6612 (OUTLIER) cc_final: 0.6375 (pp) REVERT: D 251 ASP cc_start: 0.7451 (t70) cc_final: 0.7215 (t0) REVERT: E 1184 MET cc_start: 0.5417 (tmm) cc_final: 0.5179 (tmm) outliers start: 10 outliers final: 4 residues processed: 204 average time/residue: 1.5469 time to fit residues: 345.6562 Evaluate side-chains 128 residues out of total 1726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 122 time to evaluate : 1.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 773 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 0.6980 chunk 147 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 78 optimal weight: 0.5980 chunk 152 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 113 optimal weight: 0.0870 chunk 176 optimal weight: 10.0000 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 107 GLN A 432 GLN ** A 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 HIS D 334 GLN D 340 GLN D 742 HIS D 776 ASN ** E1143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1335 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 16312 Z= 0.244 Angle : 0.632 7.383 22152 Z= 0.332 Chirality : 0.045 0.155 2325 Planarity : 0.006 0.077 2872 Dihedral : 6.613 105.970 2167 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.81 % Allowed : 7.99 % Favored : 90.20 % 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: -1.91 (0.17), residues: 1956 helix: 0.21 (0.28), residues: 305 sheet: -1.89 (0.18), residues: 585 loop : -1.28 (0.18), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 420 HIS 0.010 0.001 HIS D 812 PHE 0.014 0.001 PHE D 250 TYR 0.021 0.002 TYR A 532 ARG 0.008 0.001 ARG D 274 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 139 time to evaluate : 1.807 Fit side-chains REVERT: A 178 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8477 (mt) REVERT: A 462 LYS cc_start: 0.7903 (pptt) cc_final: 0.7659 (ptmm) REVERT: A 487 ILE cc_start: 0.8407 (OUTLIER) cc_final: 0.8195 (mp) REVERT: A 745 GLN cc_start: 0.7918 (pm20) cc_final: 0.7601 (pm20) REVERT: D 107 GLN cc_start: 0.7874 (mm110) cc_final: 0.7493 (mp10) REVERT: D 251 ASP cc_start: 0.7636 (t70) cc_final: 0.7134 (t0) outliers start: 31 outliers final: 12 residues processed: 154 average time/residue: 1.5009 time to fit residues: 254.6148 Evaluate side-chains 129 residues out of total 1726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 115 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 786 VAL Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 773 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 97 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 146 optimal weight: 2.9990 chunk 119 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 176 optimal weight: 10.0000 chunk 190 optimal weight: 40.0000 chunk 157 optimal weight: 0.4980 chunk 175 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 141 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 HIS ** A 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16312 Z= 0.256 Angle : 0.575 11.154 22152 Z= 0.295 Chirality : 0.044 0.170 2325 Planarity : 0.005 0.060 2872 Dihedral : 5.912 94.753 2162 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.45 % Allowed : 10.21 % Favored : 87.34 % 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: -1.27 (0.18), residues: 1956 helix: 0.47 (0.29), residues: 307 sheet: -1.21 (0.20), residues: 559 loop : -0.97 (0.18), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 258 HIS 0.007 0.001 HIS A 804 PHE 0.013 0.001 PHE D 153 TYR 0.017 0.001 TYR A 835 ARG 0.007 0.001 ARG D 590 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 130 time to evaluate : 2.107 Fit side-chains revert: symmetry clash REVERT: A 178 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8496 (mt) REVERT: A 462 LYS cc_start: 0.7897 (pptt) cc_final: 0.7653 (ptmm) REVERT: A 778 GLN cc_start: 0.7684 (mp10) cc_final: 0.7403 (mp10) REVERT: D 107 GLN cc_start: 0.7787 (mm110) cc_final: 0.7403 (mp10) REVERT: D 251 ASP cc_start: 0.7670 (t70) cc_final: 0.7309 (t70) REVERT: D 314 LYS cc_start: 0.8276 (mmpt) cc_final: 0.8046 (mppt) REVERT: D 394 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.8036 (mm-30) outliers start: 42 outliers final: 18 residues processed: 150 average time/residue: 1.5668 time to fit residues: 264.6708 Evaluate side-chains 129 residues out of total 1726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 109 time to evaluate : 1.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 600 SER Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 786 VAL Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 394 GLU Chi-restraints excluded: chain D residue 566 VAL Chi-restraints excluded: chain D residue 697 MET Chi-restraints excluded: chain D residue 773 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 174 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 118 optimal weight: 0.9980 chunk 177 optimal weight: 9.9990 chunk 187 optimal weight: 0.2980 chunk 92 optimal weight: 2.9990 chunk 167 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN ** A 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 GLN ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 573 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 16312 Z= 0.418 Angle : 0.625 8.391 22152 Z= 0.321 Chirality : 0.046 0.241 2325 Planarity : 0.005 0.060 2872 Dihedral : 5.633 42.918 2160 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.21 % Allowed : 11.84 % Favored : 84.95 % 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: -1.19 (0.18), residues: 1956 helix: 0.41 (0.29), residues: 305 sheet: -1.22 (0.20), residues: 585 loop : -0.81 (0.19), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 258 HIS 0.009 0.001 HIS A 804 PHE 0.015 0.002 PHE D 250 TYR 0.020 0.002 TYR A 835 ARG 0.005 0.001 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 118 time to evaluate : 1.821 Fit side-chains revert: symmetry clash REVERT: A 462 LYS cc_start: 0.7998 (pptt) cc_final: 0.7796 (ptmm) REVERT: A 778 GLN cc_start: 0.7654 (mp10) cc_final: 0.7360 (mp10) REVERT: D 71 ARG cc_start: 0.7575 (OUTLIER) cc_final: 0.5895 (ttp-170) REVERT: D 107 GLN cc_start: 0.8098 (mm110) cc_final: 0.7569 (mp10) REVERT: D 314 LYS cc_start: 0.8155 (mmpt) cc_final: 0.7930 (mppt) REVERT: D 684 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7768 (mt0) REVERT: E 1190 GLU cc_start: 0.4247 (mm-30) cc_final: 0.3771 (mm-30) REVERT: F 1215 LEU cc_start: 0.6929 (mm) cc_final: 0.6662 (mm) outliers start: 55 outliers final: 27 residues processed: 153 average time/residue: 1.4753 time to fit residues: 247.8163 Evaluate side-chains 137 residues out of total 1726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 108 time to evaluate : 1.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 600 SER Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 786 VAL Chi-restraints excluded: chain D residue 71 ARG Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 181 LYS Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 566 VAL Chi-restraints excluded: chain D residue 684 GLN Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain D residue 773 VAL Chi-restraints excluded: chain F residue 1218 LEU Chi-restraints excluded: chain F residue 1264 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 156 optimal weight: 0.7980 chunk 106 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 139 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 160 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 168 optimal weight: 6.9990 chunk 47 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 525 HIS ** A 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 395 GLN D 815 HIS ** E1143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16312 Z= 0.255 Angle : 0.548 6.196 22152 Z= 0.282 Chirality : 0.043 0.154 2325 Planarity : 0.005 0.062 2872 Dihedral : 5.412 43.399 2160 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.68 % Allowed : 13.83 % Favored : 83.49 % 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: -0.96 (0.18), residues: 1956 helix: 0.55 (0.29), residues: 307 sheet: -0.91 (0.21), residues: 557 loop : -0.77 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 210 HIS 0.005 0.001 HIS F1223 PHE 0.011 0.001 PHE D 244 TYR 0.017 0.001 TYR D 835 ARG 0.006 0.000 ARG A 405 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 117 time to evaluate : 1.946 Fit side-chains revert: symmetry clash REVERT: A 189 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.8276 (mmp) REVERT: D 71 ARG cc_start: 0.7502 (OUTLIER) cc_final: 0.5859 (ttp-170) REVERT: D 107 GLN cc_start: 0.8097 (mm110) cc_final: 0.7529 (mp10) REVERT: D 314 LYS cc_start: 0.8148 (mmpt) cc_final: 0.7923 (mppt) REVERT: D 684 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.7734 (mt0) REVERT: D 771 MET cc_start: 0.8318 (OUTLIER) cc_final: 0.7896 (mtm) REVERT: E 1189 GLU cc_start: 0.6742 (tm-30) cc_final: 0.6428 (tm-30) REVERT: E 1190 GLU cc_start: 0.4446 (mm-30) cc_final: 0.3822 (mm-30) REVERT: E 1195 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7326 (mt-10) REVERT: F 1215 LEU cc_start: 0.6972 (mm) cc_final: 0.6707 (mm) outliers start: 46 outliers final: 24 residues processed: 148 average time/residue: 1.3896 time to fit residues: 227.6573 Evaluate side-chains 132 residues out of total 1726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 104 time to evaluate : 1.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 537 GLU Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 786 VAL Chi-restraints excluded: chain A residue 796 GLU Chi-restraints excluded: chain D residue 71 ARG Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 684 GLN Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain D residue 771 MET Chi-restraints excluded: chain D residue 773 VAL Chi-restraints excluded: chain F residue 1217 VAL Chi-restraints excluded: chain F residue 1264 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 63 optimal weight: 1.9990 chunk 168 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 187 optimal weight: 0.3980 chunk 155 optimal weight: 0.6980 chunk 86 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 98 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 815 HIS ** E1143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16312 Z= 0.239 Angle : 0.533 10.401 22152 Z= 0.273 Chirality : 0.043 0.151 2325 Planarity : 0.005 0.062 2872 Dihedral : 5.269 43.915 2160 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.63 % Allowed : 14.06 % Favored : 83.31 % 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: -0.76 (0.19), residues: 1956 helix: 0.81 (0.30), residues: 301 sheet: -0.79 (0.21), residues: 557 loop : -0.67 (0.19), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 375 HIS 0.005 0.001 HIS F1223 PHE 0.011 0.001 PHE D 144 TYR 0.016 0.001 TYR D 835 ARG 0.008 0.000 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 120 time to evaluate : 1.987 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7286 (ttp80) cc_final: 0.6980 (ttt90) REVERT: A 189 MET cc_start: 0.8526 (OUTLIER) cc_final: 0.8303 (mmp) REVERT: A 778 GLN cc_start: 0.7623 (mp10) cc_final: 0.7359 (mp10) REVERT: D 71 ARG cc_start: 0.7470 (OUTLIER) cc_final: 0.5812 (ttp-170) REVERT: D 684 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.7727 (mt0) REVERT: D 771 MET cc_start: 0.8297 (OUTLIER) cc_final: 0.7888 (mtm) REVERT: E 1189 GLU cc_start: 0.6694 (tm-30) cc_final: 0.6450 (tm-30) REVERT: F 1215 LEU cc_start: 0.6931 (mm) cc_final: 0.6692 (mm) outliers start: 45 outliers final: 30 residues processed: 150 average time/residue: 1.3313 time to fit residues: 221.7705 Evaluate side-chains 140 residues out of total 1726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 106 time to evaluate : 1.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 537 GLU Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 786 VAL Chi-restraints excluded: chain A residue 796 GLU Chi-restraints excluded: chain D residue 71 ARG Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 566 VAL Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 684 GLN Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain D residue 771 MET Chi-restraints excluded: chain D residue 773 VAL Chi-restraints excluded: chain E residue 1100 VAL Chi-restraints excluded: chain F residue 1217 VAL Chi-restraints excluded: chain F residue 1264 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 180 optimal weight: 0.0030 chunk 21 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 137 optimal weight: 4.9990 chunk 158 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 186 optimal weight: 7.9990 chunk 117 optimal weight: 0.1980 chunk 113 optimal weight: 8.9990 chunk 86 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 815 HIS ** D 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16312 Z= 0.212 Angle : 0.524 7.405 22152 Z= 0.268 Chirality : 0.043 0.151 2325 Planarity : 0.004 0.066 2872 Dihedral : 5.176 43.824 2160 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.57 % Allowed : 14.41 % Favored : 83.02 % 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: -0.66 (0.19), residues: 1956 helix: 0.90 (0.30), residues: 301 sheet: -0.71 (0.21), residues: 557 loop : -0.60 (0.19), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 375 HIS 0.009 0.001 HIS D 70 PHE 0.009 0.001 PHE D 160 TYR 0.016 0.001 TYR D 835 ARG 0.013 0.000 ARG A 405 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 117 time to evaluate : 1.718 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7502 (ttp80) cc_final: 0.6900 (ttt90) REVERT: A 189 MET cc_start: 0.8493 (OUTLIER) cc_final: 0.8285 (mmp) REVERT: A 778 GLN cc_start: 0.7624 (mp10) cc_final: 0.7358 (mp10) REVERT: D 107 GLN cc_start: 0.8147 (mm110) cc_final: 0.7592 (mp10) REVERT: D 684 GLN cc_start: 0.8224 (OUTLIER) cc_final: 0.7697 (mt0) REVERT: D 771 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.7893 (mtm) REVERT: E 1190 GLU cc_start: 0.4545 (mm-30) cc_final: 0.4188 (mm-30) REVERT: E 1206 VAL cc_start: 0.6310 (p) cc_final: 0.5927 (t) REVERT: F 1215 LEU cc_start: 0.6921 (mm) cc_final: 0.6682 (mm) outliers start: 44 outliers final: 27 residues processed: 145 average time/residue: 1.3841 time to fit residues: 222.2753 Evaluate side-chains 136 residues out of total 1726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 106 time to evaluate : 1.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 537 GLU Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 786 VAL Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 566 VAL Chi-restraints excluded: chain D residue 684 GLN Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain D residue 771 MET Chi-restraints excluded: chain D residue 773 VAL Chi-restraints excluded: chain E residue 1100 VAL Chi-restraints excluded: chain F residue 1217 VAL Chi-restraints excluded: chain F residue 1218 LEU Chi-restraints excluded: chain F residue 1264 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 74 optimal weight: 0.6980 chunk 111 optimal weight: 0.6980 chunk 56 optimal weight: 0.0070 chunk 36 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 127 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 17 optimal weight: 0.0470 chunk 146 optimal weight: 0.9990 chunk 170 optimal weight: 0.8980 chunk 179 optimal weight: 0.9990 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 HIS A 815 HIS ** D 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16312 Z= 0.188 Angle : 0.514 7.275 22152 Z= 0.263 Chirality : 0.042 0.149 2325 Planarity : 0.004 0.065 2872 Dihedral : 5.036 43.590 2160 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.28 % Allowed : 15.17 % Favored : 82.56 % 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: -0.49 (0.19), residues: 1956 helix: 1.04 (0.30), residues: 301 sheet: -0.48 (0.22), residues: 531 loop : -0.58 (0.19), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 375 HIS 0.004 0.001 HIS A 812 PHE 0.010 0.001 PHE D 250 TYR 0.015 0.001 TYR D 563 ARG 0.014 0.001 ARG A 405 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 116 time to evaluate : 1.883 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7485 (ttp80) cc_final: 0.6767 (ttt90) REVERT: A 778 GLN cc_start: 0.7628 (mp10) cc_final: 0.7376 (mp10) REVERT: D 393 GLU cc_start: 0.7667 (tp30) cc_final: 0.7386 (tp30) REVERT: E 1189 GLU cc_start: 0.6759 (tm-30) cc_final: 0.6461 (tm-30) REVERT: E 1190 GLU cc_start: 0.4336 (mm-30) cc_final: 0.4095 (mm-30) REVERT: E 1206 VAL cc_start: 0.6299 (p) cc_final: 0.5912 (t) REVERT: F 1215 LEU cc_start: 0.6901 (mm) cc_final: 0.6661 (mm) REVERT: F 1218 LEU cc_start: 0.7393 (OUTLIER) cc_final: 0.7167 (pt) outliers start: 39 outliers final: 19 residues processed: 142 average time/residue: 1.4406 time to fit residues: 225.5673 Evaluate side-chains 130 residues out of total 1726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 110 time to evaluate : 1.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 786 VAL Chi-restraints excluded: chain A residue 796 GLU Chi-restraints excluded: chain D residue 42 ARG Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain D residue 773 VAL Chi-restraints excluded: chain F residue 1218 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 1.9990 chunk 174 optimal weight: 0.6980 chunk 179 optimal weight: 2.9990 chunk 104 optimal weight: 0.0170 chunk 75 optimal weight: 0.0980 chunk 136 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 157 optimal weight: 0.0570 chunk 164 optimal weight: 0.5980 chunk 173 optimal weight: 6.9990 chunk 114 optimal weight: 0.9990 overall best weight: 0.2936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN A 68 HIS ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 107 GLN ** D 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 16312 Z= 0.161 Angle : 0.501 7.487 22152 Z= 0.256 Chirality : 0.042 0.147 2325 Planarity : 0.004 0.065 2872 Dihedral : 4.907 43.385 2160 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.52 % Allowed : 16.10 % Favored : 82.38 % 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: -0.40 (0.19), residues: 1956 helix: 1.10 (0.30), residues: 309 sheet: -0.39 (0.22), residues: 527 loop : -0.54 (0.19), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 375 HIS 0.004 0.001 HIS D 70 PHE 0.015 0.001 PHE D 144 TYR 0.015 0.001 TYR D 563 ARG 0.015 0.000 ARG A 405 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 126 time to evaluate : 1.839 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7391 (ttp80) cc_final: 0.6727 (ttt90) REVERT: A 552 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8366 (mmt) REVERT: A 778 GLN cc_start: 0.7632 (mp10) cc_final: 0.7378 (mp10) REVERT: D 107 GLN cc_start: 0.8168 (mm110) cc_final: 0.7630 (mp10) REVERT: D 314 LYS cc_start: 0.8246 (tppp) cc_final: 0.7989 (mppt) REVERT: D 393 GLU cc_start: 0.7659 (tp30) cc_final: 0.7386 (tp30) REVERT: E 1184 MET cc_start: 0.5647 (tmm) cc_final: 0.5395 (tmm) REVERT: E 1189 GLU cc_start: 0.6635 (tm-30) cc_final: 0.6271 (tm-30) REVERT: E 1206 VAL cc_start: 0.6127 (p) cc_final: 0.5903 (t) REVERT: F 1215 LEU cc_start: 0.6822 (mm) cc_final: 0.6568 (mm) REVERT: F 1218 LEU cc_start: 0.7418 (OUTLIER) cc_final: 0.6965 (pp) outliers start: 26 outliers final: 15 residues processed: 144 average time/residue: 1.4364 time to fit residues: 228.6920 Evaluate side-chains 130 residues out of total 1726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 113 time to evaluate : 1.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 786 VAL Chi-restraints excluded: chain D residue 42 ARG Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain D residue 773 VAL Chi-restraints excluded: chain F residue 1218 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 184 optimal weight: 9.9990 chunk 112 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 chunk 128 optimal weight: 0.8980 chunk 193 optimal weight: 20.0000 chunk 177 optimal weight: 10.0000 chunk 153 optimal weight: 0.6980 chunk 15 optimal weight: 0.1980 chunk 118 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 122 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 HIS ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16312 Z= 0.243 Angle : 0.530 7.598 22152 Z= 0.271 Chirality : 0.043 0.150 2325 Planarity : 0.005 0.063 2872 Dihedral : 4.997 44.549 2160 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.58 % Allowed : 16.45 % Favored : 81.97 % 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: -0.40 (0.19), residues: 1956 helix: 1.03 (0.30), residues: 309 sheet: -0.40 (0.22), residues: 539 loop : -0.51 (0.19), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 375 HIS 0.009 0.001 HIS A 68 PHE 0.013 0.001 PHE D 472 TYR 0.017 0.001 TYR D 563 ARG 0.015 0.001 ARG A 405 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 113 time to evaluate : 1.873 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7322 (ttp80) cc_final: 0.6790 (ttt90) REVERT: A 171 MET cc_start: 0.8690 (ptm) cc_final: 0.8451 (ppp) REVERT: A 552 MET cc_start: 0.8675 (OUTLIER) cc_final: 0.8389 (mmt) REVERT: A 778 GLN cc_start: 0.7624 (mp10) cc_final: 0.7377 (mp10) REVERT: D 107 GLN cc_start: 0.8153 (mm110) cc_final: 0.7560 (mp10) REVERT: D 314 LYS cc_start: 0.8215 (tppp) cc_final: 0.7980 (tppt) REVERT: D 393 GLU cc_start: 0.7674 (tp30) cc_final: 0.7423 (tp30) REVERT: E 1189 GLU cc_start: 0.6621 (tm-30) cc_final: 0.6418 (tm-30) REVERT: F 1215 LEU cc_start: 0.6868 (mm) cc_final: 0.6641 (mm) REVERT: F 1218 LEU cc_start: 0.7402 (OUTLIER) cc_final: 0.7035 (pp) outliers start: 27 outliers final: 16 residues processed: 133 average time/residue: 1.4855 time to fit residues: 217.2432 Evaluate side-chains 128 residues out of total 1726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 110 time to evaluate : 1.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 786 VAL Chi-restraints excluded: chain D residue 42 ARG Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain D residue 773 VAL Chi-restraints excluded: chain F residue 1218 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 0.9990 chunk 47 optimal weight: 0.4980 chunk 141 optimal weight: 0.2980 chunk 22 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 154 optimal weight: 0.4980 chunk 64 optimal weight: 1.9990 chunk 158 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 28 optimal weight: 0.0170 chunk 135 optimal weight: 3.9990 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 HIS ** A 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 HIS ** 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 = 0.3904 r_free = 0.3904 target = 0.147392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.102199 restraints weight = 21526.167| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.54 r_work: 0.3136 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2997 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2996 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16312 Z= 0.178 Angle : 0.513 9.397 22152 Z= 0.261 Chirality : 0.042 0.148 2325 Planarity : 0.004 0.065 2872 Dihedral : 4.890 40.914 2158 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.34 % Allowed : 16.74 % Favored : 81.91 % 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: -0.36 (0.19), residues: 1956 helix: 1.10 (0.30), residues: 309 sheet: -0.34 (0.23), residues: 531 loop : -0.51 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 375 HIS 0.006 0.001 HIS A 68 PHE 0.012 0.001 PHE D 144 TYR 0.015 0.001 TYR D 835 ARG 0.015 0.001 ARG A 405 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5320.58 seconds wall clock time: 96 minutes 4.24 seconds (5764.24 seconds total)