Starting phenix.real_space_refine on Fri Aug 9 07:09:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8toa_41441/08_2024/8toa_41441.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8toa_41441/08_2024/8toa_41441.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8toa_41441/08_2024/8toa_41441.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8toa_41441/08_2024/8toa_41441.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8toa_41441/08_2024/8toa_41441.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8toa_41441/08_2024/8toa_41441.cif" } resolution = 3.69 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= 0.001 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 11061 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 93 5.16 5 C 10339 2.51 5 N 2867 2.21 5 O 3271 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H GLU 64": "OE1" <-> "OE2" Residue "D GLU 64": "OE1" <-> "OE2" Residue "A GLU 46": "OE1" <-> "OE2" Residue "A GLU 64": "OE1" <-> "OE2" Residue "B PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 71": "OE1" <-> "OE2" Residue "C GLU 79": "OE1" <-> "OE2" Residue "C GLU 390": "OE1" <-> "OE2" Residue "C GLU 424": "OE1" <-> "OE2" Residue "C GLU 435": "OE1" <-> "OE2" Residue "I GLU 95": "OE1" <-> "OE2" Residue "I GLU 385": "OE1" <-> "OE2" Residue "K GLU 34": "OE1" <-> "OE2" Residue "K GLU 385": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 16570 Number of models: 1 Model: "" Number of chains: 15 Chain: "H" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 925 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 112} Chain: "L" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 848 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 101} Chain: "D" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 925 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 112} Chain: "E" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 848 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 101} Chain: "A" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 925 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 112} Chain: "B" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 848 Classifications: {'peptide': 111} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 101} Chain: "C" Number of atoms: 3699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3699 Classifications: {'peptide': 473} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 459} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "I" Number of atoms: 3699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3699 Classifications: {'peptide': 473} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 459} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "K" Number of atoms: 3699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3699 Classifications: {'peptide': 473} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 459} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "L" 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: "E" 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: 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: "C" 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: "I" 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: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 8.60, per 1000 atoms: 0.52 Number of scatterers: 16570 At special positions: 0 Unit cell: (140.27, 138.61, 159.36, 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 93 16.00 O 3271 8.00 N 2867 7.00 C 10339 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 93 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 95 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 93 " distance=2.04 Simple disulfide: pdb=" SG CYS C 4 " - pdb=" SG CYS C 458 " distance=2.03 Simple disulfide: pdb=" SG CYS C 42 " - pdb=" SG CYS C 268 " distance=2.04 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 66 " distance=2.02 Simple disulfide: pdb=" SG CYS C 87 " - pdb=" SG CYS C 129 " distance=2.03 Simple disulfide: pdb=" SG CYS C 272 " - pdb=" SG CYS C 296 " distance=2.03 Simple disulfide: pdb=" SG CYS C 465 " - pdb=" SG CYS C 469 " distance=2.02 Simple disulfide: pdb=" SG CYS I 4 " - pdb=" SG CYS I 458 " distance=2.03 Simple disulfide: pdb=" SG CYS I 42 " - pdb=" SG CYS I 268 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 66 " distance=2.02 Simple disulfide: pdb=" SG CYS I 87 " - pdb=" SG CYS I 129 " distance=2.03 Simple disulfide: pdb=" SG CYS I 272 " - pdb=" SG CYS I 296 " distance=2.03 Simple disulfide: pdb=" SG CYS I 465 " - pdb=" SG CYS I 469 " distance=2.03 Simple disulfide: pdb=" SG CYS K 4 " - pdb=" SG CYS K 458 " distance=2.03 Simple disulfide: pdb=" SG CYS K 42 " - pdb=" SG CYS K 268 " distance=2.04 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 66 " distance=2.03 Simple disulfide: pdb=" SG CYS K 87 " - pdb=" SG CYS K 129 " distance=2.03 Simple disulfide: pdb=" SG CYS K 272 " - pdb=" SG CYS K 296 " distance=2.03 Simple disulfide: pdb=" SG CYS K 465 " - pdb=" SG CYS K 469 " 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 NAG-ASN " NAG B 201 " - " ASN B 26 " " NAG C 601 " - " ASN C 28 " " NAG C 602 " - " ASN C 403 " " NAG C 603 " - " ASN C 231 " " NAG E 201 " - " ASN E 26 " " NAG I 601 " - " ASN I 403 " " NAG I 602 " - " ASN I 28 " " NAG I 603 " - " ASN I 231 " " NAG K 601 " - " ASN K 403 " " NAG K 602 " - " ASN K 28 " " NAG L 201 " - " ASN L 26 " Time building additional restraints: 5.81 Conformation dependent library (CDL) restraints added in 3.1 seconds 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3816 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 44 sheets defined 18.7% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.26 Creating SS restraints... Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'L' and resid 84 through 88 removed outlier: 3.593A pdb=" N ASP L 87 " --> pdb=" O GLU L 84 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N VAL L 88 " --> pdb=" O ALA L 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 84 through 88' Processing helix chain 'D' and resid 86 through 90 Processing helix chain 'E' and resid 84 through 88 removed outlier: 3.594A pdb=" N ASP E 87 " --> pdb=" O GLU E 84 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N VAL E 88 " --> pdb=" O ALA E 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 84 through 88' Processing helix chain 'A' and resid 86 through 90 Processing helix chain 'C' and resid 57 through 62 removed outlier: 3.985A pdb=" N THR C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 67 removed outlier: 4.109A pdb=" N ASP C 67 " --> pdb=" O PRO C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 104 Processing helix chain 'C' and resid 178 through 186 Processing helix chain 'C' and resid 358 through 377 Processing helix chain 'C' and resid 395 through 448 removed outlier: 5.254A pdb=" N GLU C 435 " --> pdb=" O LEU C 431 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N MET C 436 " --> pdb=" O ALA C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 451 No H-bonds generated for 'chain 'C' and resid 449 through 451' Processing helix chain 'C' and resid 466 through 475 Processing helix chain 'C' and resid 483 through 489 removed outlier: 4.114A pdb=" N GLN C 489 " --> pdb=" O GLU C 485 " (cutoff:3.500A) Processing helix chain 'I' and resid 57 through 62 removed outlier: 4.014A pdb=" N THR I 61 " --> pdb=" O LEU I 57 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 67 removed outlier: 4.111A pdb=" N ASP I 67 " --> pdb=" O PRO I 64 " (cutoff:3.500A) Processing helix chain 'I' and resid 94 through 104 removed outlier: 3.763A pdb=" N LEU I 98 " --> pdb=" O ASN I 94 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU I 104 " --> pdb=" O GLN I 100 " (cutoff:3.500A) Processing helix chain 'I' and resid 178 through 186 Processing helix chain 'I' and resid 358 through 377 removed outlier: 3.977A pdb=" N SER I 364 " --> pdb=" O LYS I 360 " (cutoff:3.500A) Processing helix chain 'I' and resid 395 through 448 Processing helix chain 'I' and resid 466 through 475 Processing helix chain 'I' and resid 479 through 489 removed outlier: 4.479A pdb=" N TYR I 483 " --> pdb=" O ASP I 479 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N GLU I 485 " --> pdb=" O SER I 481 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N GLU I 486 " --> pdb=" O LYS I 482 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N GLN I 489 " --> pdb=" O GLU I 485 " (cutoff:3.500A) Processing helix chain 'K' and resid 57 through 62 removed outlier: 4.039A pdb=" N THR K 61 " --> pdb=" O LEU K 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 63 through 67 removed outlier: 3.899A pdb=" N ASP K 67 " --> pdb=" O PRO K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 94 through 105 removed outlier: 3.807A pdb=" N LEU K 98 " --> pdb=" O ASN K 94 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU K 104 " --> pdb=" O GLN K 100 " (cutoff:3.500A) Processing helix chain 'K' and resid 178 through 186 Processing helix chain 'K' and resid 358 through 378 removed outlier: 4.489A pdb=" N SER K 364 " --> pdb=" O LYS K 360 " (cutoff:3.500A) Processing helix chain 'K' and resid 395 through 447 Processing helix chain 'K' and resid 468 through 473 removed outlier: 3.831A pdb=" N ILE K 473 " --> pdb=" O CYS K 469 " (cutoff:3.500A) Processing helix chain 'K' and resid 484 through 490 Processing sheet with id=AA1, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AA3, first strand: chain 'H' and resid 57 through 59 removed outlier: 3.594A pdb=" N GLU H 46 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ALA H 96 " --> pdb=" O SER H 35 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 92 through 93 removed outlier: 3.720A pdb=" N TYR H 93 " --> pdb=" O THR H 113 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.713A pdb=" N SER L 7 " --> pdb=" O SER L 22 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 12 removed outlier: 5.953A pdb=" N LEU L 11 " --> pdb=" O ASP L 110 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL L 109 " --> pdb=" O GLY L 89 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY L 89 " --> pdb=" O VAL L 109 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE L 53 " --> pdb=" O TRP L 40 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ARG L 42 " --> pdb=" O LEU L 51 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N LEU L 51 " --> pdb=" O ARG L 42 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR L 54 " --> pdb=" O ASN L 58 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AA8, first strand: chain 'D' and resid 11 through 12 Processing sheet with id=AA9, first strand: chain 'D' and resid 57 through 59 removed outlier: 3.593A pdb=" N GLU D 46 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TRP D 36 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA D 96 " --> pdb=" O SER D 35 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 92 through 93 removed outlier: 3.719A pdb=" N TYR D 93 " --> pdb=" O THR D 113 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.713A pdb=" N SER E 7 " --> pdb=" O SER E 22 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.953A pdb=" N LEU E 11 " --> pdb=" O ASP E 110 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL E 109 " --> pdb=" O GLY E 89 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY E 89 " --> pdb=" O VAL E 109 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE E 53 " --> pdb=" O TRP E 40 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ARG E 42 " --> pdb=" O LEU E 51 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N LEU E 51 " --> pdb=" O ARG E 42 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR E 54 " --> pdb=" O ASN E 58 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 4 through 7 Processing sheet with id=AB5, first strand: chain 'A' and resid 57 through 59 removed outlier: 6.534A pdb=" N TRP A 36 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA A 96 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE A 94 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR A 93 " --> pdb=" O THR A 113 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 67 through 69 Processing sheet with id=AB7, first strand: chain 'B' and resid 4 through 7 Processing sheet with id=AB8, first strand: chain 'B' and resid 10 through 12 removed outlier: 3.633A pdb=" N LEU B 11 " --> pdb=" O THR B 108 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL B 109 " --> pdb=" O GLY B 89 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLY B 89 " --> pdb=" O VAL B 109 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AC1, first strand: chain 'C' and resid 352 through 356 removed outlier: 3.674A pdb=" N GLY C 352 " --> pdb=" O ASN C 349 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG C 346 " --> pdb=" O CYS C 4 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N CYS C 4 " --> pdb=" O ARG C 346 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N GLN C 348 " --> pdb=" O LYS C 2 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N LYS C 2 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 14 through 16 removed outlier: 3.898A pdb=" N THR C 14 " --> pdb=" O VAL C 26 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 33 through 34 Processing sheet with id=AC4, first strand: chain 'C' and resid 49 through 50 Processing sheet with id=AC5, first strand: chain 'C' and resid 91 through 92 removed outlier: 3.832A pdb=" N PHE C 223 " --> pdb=" O LYS C 91 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TRP C 171 " --> pdb=" O HIS C 224 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 108 through 109 Processing sheet with id=AC7, first strand: chain 'C' and resid 140 through 141 Processing sheet with id=AC8, first strand: chain 'C' and resid 158 through 160 Processing sheet with id=AC9, first strand: chain 'C' and resid 272 through 274 removed outlier: 3.691A pdb=" N CYS C 272 " --> pdb=" O ILE C 279 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY C 277 " --> pdb=" O TYR C 274 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 2 through 3 removed outlier: 3.741A pdb=" N ILE I 3 " --> pdb=" O PHE I 459 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 14 through 16 removed outlier: 3.973A pdb=" N THR I 14 " --> pdb=" O VAL I 26 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL I 26 " --> pdb=" O THR I 14 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 33 through 34 Processing sheet with id=AD4, first strand: chain 'I' and resid 50 through 52 Processing sheet with id=AD5, first strand: chain 'I' and resid 140 through 142 removed outlier: 8.387A pdb=" N VAL I 170 " --> pdb=" O PRO I 245 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TRP I 171 " --> pdb=" O HIS I 224 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 140 through 142 removed outlier: 8.387A pdb=" N VAL I 170 " --> pdb=" O PRO I 245 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 203 through 204 removed outlier: 3.777A pdb=" N VAL I 193 " --> pdb=" O PHE I 204 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 272 through 274 removed outlier: 3.693A pdb=" N CYS I 272 " --> pdb=" O ILE I 279 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY I 277 " --> pdb=" O TYR I 274 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 14 through 16 removed outlier: 3.890A pdb=" N THR K 14 " --> pdb=" O VAL K 26 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL K 26 " --> pdb=" O THR K 14 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 30 through 31 Processing sheet with id=AE2, first strand: chain 'K' and resid 33 through 34 Processing sheet with id=AE3, first strand: chain 'K' and resid 49 through 50 removed outlier: 6.341A pdb=" N ILE K 77 " --> pdb=" O ILE K 258 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 90 through 92 removed outlier: 7.445A pdb=" N LYS K 91 " --> pdb=" O PHE K 223 " (cutoff:3.500A) removed outlier: 9.055A pdb=" N TRP K 225 " --> pdb=" O LYS K 91 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TRP K 171 " --> pdb=" O HIS K 224 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N SER K 249 " --> pdb=" O LEU K 168 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N VAL K 170 " --> pdb=" O ARG K 247 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N ARG K 247 " --> pdb=" O VAL K 170 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 121 through 124 removed outlier: 4.626A pdb=" N ASN K 123 " --> pdb=" O TRP K 142 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N TRP K 142 " --> pdb=" O ASN K 123 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 158 through 160 Processing sheet with id=AE7, first strand: chain 'K' and resid 277 through 278 removed outlier: 3.703A pdb=" N GLY K 277 " --> pdb=" O TYR K 274 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 451 through 452 removed outlier: 3.545A pdb=" N GLU K 452 " --> pdb=" O GLU K 460 " (cutoff:3.500A) 478 hydrogen bonds defined for protein. 1269 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: 5.43 Time building geometry restraints manager: 6.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5110 1.34 - 1.46: 3854 1.46 - 1.58: 7822 1.58 - 1.71: 0 1.71 - 1.83: 132 Bond restraints: 16918 Sorted by residual: bond pdb=" N VAL K 10 " pdb=" CA VAL K 10 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.11e-02 8.12e+03 1.32e+01 bond pdb=" CA PRO A 40 " pdb=" C PRO A 40 " ideal model delta sigma weight residual 1.514 1.534 -0.020 5.50e-03 3.31e+04 1.32e+01 bond pdb=" N VAL A 37 " pdb=" CA VAL A 37 " ideal model delta sigma weight residual 1.456 1.495 -0.040 1.11e-02 8.12e+03 1.28e+01 bond pdb=" N VAL A 115 " pdb=" CA VAL A 115 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.11e-02 8.12e+03 1.24e+01 bond pdb=" N ILE B 53 " pdb=" CA ILE B 53 " ideal model delta sigma weight residual 1.458 1.497 -0.040 1.18e-02 7.18e+03 1.13e+01 ... (remaining 16913 not shown) Histogram of bond angle deviations from ideal: 97.57 - 104.92: 281 104.92 - 112.27: 7977 112.27 - 119.62: 6307 119.62 - 126.98: 8153 126.98 - 134.33: 189 Bond angle restraints: 22907 Sorted by residual: angle pdb=" CA GLY B 106 " pdb=" C GLY B 106 " pdb=" O GLY B 106 " ideal model delta sigma weight residual 122.22 118.31 3.91 6.50e-01 2.37e+00 3.61e+01 angle pdb=" CA GLY B 71 " pdb=" C GLY B 71 " pdb=" O GLY B 71 " ideal model delta sigma weight residual 122.52 117.92 4.60 7.90e-01 1.60e+00 3.39e+01 angle pdb=" C ASN C 475 " pdb=" N ASN C 476 " pdb=" CA ASN C 476 " ideal model delta sigma weight residual 121.54 131.55 -10.01 1.91e+00 2.74e-01 2.75e+01 angle pdb=" N GLU I 435 " pdb=" CA GLU I 435 " pdb=" CB GLU I 435 " ideal model delta sigma weight residual 110.28 118.01 -7.73 1.55e+00 4.16e-01 2.49e+01 angle pdb=" N THR I 477 " pdb=" CA THR I 477 " pdb=" C THR I 477 " ideal model delta sigma weight residual 114.56 108.36 6.20 1.27e+00 6.20e-01 2.38e+01 ... (remaining 22902 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.41: 9683 26.41 - 52.82: 484 52.82 - 79.23: 55 79.23 - 105.64: 7 105.64 - 132.04: 1 Dihedral angle restraints: 10230 sinusoidal: 4233 harmonic: 5997 Sorted by residual: dihedral pdb=" CA THR B 99 " pdb=" C THR B 99 " pdb=" N PRO B 100 " pdb=" CA PRO B 100 " ideal model delta harmonic sigma weight residual 180.00 47.96 132.04 0 5.00e+00 4.00e-02 6.97e+02 dihedral pdb=" CB CYS K 465 " pdb=" SG CYS K 465 " pdb=" SG CYS K 469 " pdb=" CB CYS K 469 " ideal model delta sinusoidal sigma weight residual -86.00 -174.22 88.22 1 1.00e+01 1.00e-02 9.30e+01 dihedral pdb=" CB CYS C 42 " pdb=" SG CYS C 42 " pdb=" SG CYS C 268 " pdb=" CB CYS C 268 " ideal model delta sinusoidal sigma weight residual -86.00 1.78 -87.78 1 1.00e+01 1.00e-02 9.23e+01 ... (remaining 10227 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 2074 0.083 - 0.167: 380 0.167 - 0.250: 38 0.250 - 0.334: 2 0.334 - 0.417: 3 Chirality restraints: 2497 Sorted by residual: chirality pdb=" CB ILE C 279 " pdb=" CA ILE C 279 " pdb=" CG1 ILE C 279 " pdb=" CG2 ILE C 279 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.42 2.00e-01 2.50e+01 4.35e+00 chirality pdb=" CB ILE I 279 " pdb=" CA ILE I 279 " pdb=" CG1 ILE I 279 " pdb=" CG2 ILE I 279 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.69e+00 chirality pdb=" CB VAL I 234 " pdb=" CA VAL I 234 " pdb=" CG1 VAL I 234 " pdb=" CG2 VAL I 234 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.03e+00 ... (remaining 2494 not shown) Planarity restraints: 3007 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR I 273 " 0.016 2.00e-02 2.50e+03 2.64e-02 1.40e+01 pdb=" CG TYR I 273 " -0.063 2.00e-02 2.50e+03 pdb=" CD1 TYR I 273 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR I 273 " 0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR I 273 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR I 273 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR I 273 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR I 273 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO C 63 " -0.048 5.00e-02 4.00e+02 7.35e-02 8.65e+00 pdb=" N PRO C 64 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO C 64 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 64 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE I 38 " -0.045 5.00e-02 4.00e+02 6.86e-02 7.53e+00 pdb=" N PRO I 39 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO I 39 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO I 39 " -0.038 5.00e-02 4.00e+02 ... (remaining 3004 not shown) Histogram of nonbonded interaction distances: 1.05 - 1.82: 14 1.82 - 2.59: 201 2.59 - 3.36: 20633 3.36 - 4.13: 40965 4.13 - 4.90: 71697 Nonbonded interactions: 133510 Sorted by model distance: nonbonded pdb=" OD2 ASP D 107 " pdb=" CD1 TRP D 109 " model vdw 1.051 3.260 nonbonded pdb=" OD2 ASP H 107 " pdb=" CD1 TRP H 109 " model vdw 1.051 3.260 nonbonded pdb=" N TYR H 104 " pdb=" NZ LYS C 157 " model vdw 1.223 3.200 nonbonded pdb=" OD2 ASP H 107 " pdb=" CG TRP H 109 " model vdw 1.308 3.260 nonbonded pdb=" OD2 ASP D 107 " pdb=" CG TRP D 109 " model vdw 1.308 3.260 ... (remaining 133505 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'L' } ncs_group { reference = (chain 'C' and (resid 1 through 490 or resid 601 through 602)) selection = (chain 'I' and (resid 1 through 490 or resid 601 through 602)) selection = chain 'K' } 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: 4.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.160 Construct map_model_manager: 0.010 Extract box with map and model: 0.720 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 45.080 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.100 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6318 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 : 0.007 0.047 16918 Z= 0.438 Angle : 1.075 14.256 22907 Z= 0.654 Chirality : 0.063 0.417 2497 Planarity : 0.007 0.078 2996 Dihedral : 14.713 132.044 6342 Min Nonbonded Distance : 1.051 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.41 % Favored : 92.30 % Rotamer: Outliers : 1.62 % Allowed : 2.95 % Favored : 95.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % Cis-general : 0.00 % Twisted Proline : 1.19 % 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 (0.16), residues: 2079 helix: -0.74 (0.25), residues: 318 sheet: -2.32 (0.24), residues: 423 loop : -2.11 (0.14), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP K 404 HIS 0.020 0.002 HIS I 8 PHE 0.034 0.003 PHE E 103 TYR 0.063 0.003 TYR I 273 ARG 0.017 0.001 ARG D 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 1797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 445 time to evaluate : 1.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 LEU cc_start: 0.8330 (tp) cc_final: 0.8041 (tt) REVERT: B 57 PHE cc_start: 0.7648 (OUTLIER) cc_final: 0.7299 (p90) REVERT: B 95 GLN cc_start: 0.7214 (OUTLIER) cc_final: 0.6580 (pt0) REVERT: K 43 SER cc_start: 0.7355 (p) cc_final: 0.7062 (p) REVERT: K 488 MET cc_start: 0.6358 (ttp) cc_final: 0.5963 (ttp) outliers start: 29 outliers final: 0 residues processed: 457 average time/residue: 0.2830 time to fit residues: 192.1862 Evaluate side-chains 319 residues out of total 1797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 317 time to evaluate : 1.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 95 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 6.9990 chunk 156 optimal weight: 9.9990 chunk 87 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 162 optimal weight: 5.9990 chunk 62 optimal weight: 0.6980 chunk 98 optimal weight: 0.9990 chunk 120 optimal weight: 0.9980 chunk 187 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 1 GLN H 30 ASN D 1 GLN D 30 ASN A 1 GLN A 30 ASN A 39 GLN B 6 GLN B 98 GLN C 7 HIS C 259 GLN I 259 GLN I 463 HIS K 425 ASN ** K 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6449 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16918 Z= 0.213 Angle : 0.716 13.301 22907 Z= 0.371 Chirality : 0.044 0.176 2497 Planarity : 0.005 0.097 2996 Dihedral : 6.876 67.031 2531 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.72 % Favored : 94.13 % Rotamer: Outliers : 2.79 % Allowed : 12.49 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.05 % 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: -2.40 (0.17), residues: 2079 helix: 0.20 (0.28), residues: 324 sheet: -2.07 (0.22), residues: 507 loop : -1.93 (0.15), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP I 342 HIS 0.012 0.001 HIS I 463 PHE 0.028 0.002 PHE E 57 TYR 0.032 0.002 TYR A 32 ARG 0.005 0.001 ARG A 97 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 355 time to evaluate : 1.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 9 LEU cc_start: 0.8824 (tp) cc_final: 0.8238 (tt) REVERT: L 38 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7269 (mt) REVERT: B 9 LEU cc_start: 0.8567 (tp) cc_final: 0.8341 (tt) REVERT: B 57 PHE cc_start: 0.7665 (OUTLIER) cc_final: 0.7405 (p90) REVERT: C 298 ARG cc_start: 0.7423 (mpt180) cc_final: 0.7179 (mpt180) REVERT: I 113 MET cc_start: 0.7071 (ttm) cc_final: 0.6823 (ttm) REVERT: K 43 SER cc_start: 0.7284 (p) cc_final: 0.6990 (p) REVERT: K 488 MET cc_start: 0.6385 (ttp) cc_final: 0.5978 (ttp) outliers start: 50 outliers final: 30 residues processed: 375 average time/residue: 0.2692 time to fit residues: 152.6483 Evaluate side-chains 330 residues out of total 1797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 298 time to evaluate : 1.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 34 TRP Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 94 MET Chi-restraints excluded: chain D residue 53 TYR Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 57 PHE Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain B residue 47 GLN Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain I residue 262 VAL Chi-restraints excluded: chain I residue 307 LEU Chi-restraints excluded: chain I residue 313 ASN Chi-restraints excluded: chain I residue 401 VAL Chi-restraints excluded: chain I residue 439 LEU Chi-restraints excluded: chain I residue 445 ARG Chi-restraints excluded: chain K residue 143 LEU Chi-restraints excluded: chain K residue 401 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 104 optimal weight: 0.9990 chunk 58 optimal weight: 10.0000 chunk 156 optimal weight: 8.9990 chunk 128 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 188 optimal weight: 0.0980 chunk 203 optimal weight: 9.9990 chunk 167 optimal weight: 4.9990 chunk 186 optimal weight: 0.6980 chunk 64 optimal weight: 5.9990 chunk 151 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 5 GLN L 43 GLN E 43 GLN C 259 GLN ** I 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 347 HIS K 425 ASN ** K 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6620 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 16918 Z= 0.284 Angle : 0.694 10.214 22907 Z= 0.361 Chirality : 0.045 0.358 2497 Planarity : 0.005 0.077 2996 Dihedral : 6.408 57.188 2531 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.59 % Favored : 93.27 % Rotamer: Outliers : 3.18 % Allowed : 15.83 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % Cis-general : 0.00 % Twisted Proline : 1.19 % 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: -2.27 (0.17), residues: 2079 helix: 0.53 (0.29), residues: 324 sheet: -2.16 (0.21), residues: 522 loop : -1.81 (0.16), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP I 342 HIS 0.010 0.002 HIS C 224 PHE 0.028 0.002 PHE K 115 TYR 0.026 0.002 TYR H 32 ARG 0.004 0.000 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 335 time to evaluate : 1.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 9 LEU cc_start: 0.8818 (tp) cc_final: 0.8243 (tt) REVERT: L 28 SER cc_start: 0.7134 (t) cc_final: 0.6920 (m) REVERT: B 9 LEU cc_start: 0.8658 (tp) cc_final: 0.8247 (tt) REVERT: B 95 GLN cc_start: 0.6959 (OUTLIER) cc_final: 0.6308 (pp30) REVERT: C 144 LEU cc_start: 0.7587 (mp) cc_final: 0.7360 (mt) REVERT: I 113 MET cc_start: 0.6985 (ttm) cc_final: 0.6627 (ttm) REVERT: K 43 SER cc_start: 0.7086 (p) cc_final: 0.6864 (p) REVERT: K 488 MET cc_start: 0.6358 (ttp) cc_final: 0.5976 (ttp) outliers start: 57 outliers final: 38 residues processed: 362 average time/residue: 0.2719 time to fit residues: 149.3575 Evaluate side-chains 338 residues out of total 1797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 299 time to evaluate : 1.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 34 TRP Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain D residue 53 TYR Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 57 PHE Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain I residue 249 SER Chi-restraints excluded: chain I residue 262 VAL Chi-restraints excluded: chain I residue 313 ASN Chi-restraints excluded: chain I residue 347 HIS Chi-restraints excluded: chain I residue 423 MET Chi-restraints excluded: chain I residue 445 ARG Chi-restraints excluded: chain K residue 104 GLU Chi-restraints excluded: chain K residue 221 ILE Chi-restraints excluded: chain K residue 307 LEU Chi-restraints excluded: chain K residue 367 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 186 optimal weight: 4.9990 chunk 141 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 126 optimal weight: 6.9990 chunk 188 optimal weight: 1.9990 chunk 200 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 chunk 179 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 GLN C 427 HIS ** I 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 426 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6615 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16918 Z= 0.224 Angle : 0.676 11.550 22907 Z= 0.345 Chirality : 0.044 0.281 2497 Planarity : 0.005 0.078 2996 Dihedral : 6.125 56.122 2529 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.01 % Favored : 93.84 % Rotamer: Outliers : 3.46 % Allowed : 18.17 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.05 % 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: -2.16 (0.17), residues: 2079 helix: 0.79 (0.29), residues: 324 sheet: -2.10 (0.22), residues: 483 loop : -1.81 (0.16), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 47 HIS 0.012 0.001 HIS I 347 PHE 0.022 0.002 PHE E 76 TYR 0.022 0.002 TYR H 32 ARG 0.004 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 331 time to evaluate : 1.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 9 LEU cc_start: 0.8749 (tp) cc_final: 0.8126 (tt) REVERT: L 55 LEU cc_start: 0.7538 (mt) cc_final: 0.7258 (tp) REVERT: L 94 MET cc_start: 0.7397 (OUTLIER) cc_final: 0.6821 (tpt) REVERT: E 30 GLN cc_start: 0.6269 (tp-100) cc_final: 0.5873 (tp-100) REVERT: B 9 LEU cc_start: 0.8681 (tp) cc_final: 0.8229 (tt) REVERT: B 95 GLN cc_start: 0.6759 (OUTLIER) cc_final: 0.6552 (pp30) REVERT: C 104 GLU cc_start: 0.7292 (mt-10) cc_final: 0.7082 (tt0) REVERT: I 113 MET cc_start: 0.6981 (ttm) cc_final: 0.6684 (ttm) REVERT: K 43 SER cc_start: 0.7378 (p) cc_final: 0.7098 (p) REVERT: K 488 MET cc_start: 0.6247 (ttp) cc_final: 0.5863 (ttp) outliers start: 62 outliers final: 38 residues processed: 361 average time/residue: 0.2480 time to fit residues: 135.4601 Evaluate side-chains 345 residues out of total 1797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 305 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 34 TRP Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 94 MET Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 313 ASN Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain I residue 193 VAL Chi-restraints excluded: chain I residue 194 THR Chi-restraints excluded: chain I residue 221 ILE Chi-restraints excluded: chain I residue 235 THR Chi-restraints excluded: chain I residue 249 SER Chi-restraints excluded: chain I residue 262 VAL Chi-restraints excluded: chain I residue 264 VAL Chi-restraints excluded: chain I residue 313 ASN Chi-restraints excluded: chain I residue 445 ARG Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain K residue 143 LEU Chi-restraints excluded: chain K residue 205 VAL Chi-restraints excluded: chain K residue 221 ILE Chi-restraints excluded: chain K residue 367 ASP Chi-restraints excluded: chain K residue 369 ILE Chi-restraints excluded: chain K residue 426 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 166 optimal weight: 1.9990 chunk 113 optimal weight: 7.9990 chunk 2 optimal weight: 0.9980 chunk 148 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 170 optimal weight: 0.9980 chunk 138 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 179 optimal weight: 0.0370 chunk 50 optimal weight: 0.3980 overall best weight: 0.8860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: