Starting phenix.real_space_refine on Sat Feb 17 23:16:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dkj_30707/02_2024/7dkj_30707.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dkj_30707/02_2024/7dkj_30707.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dkj_30707/02_2024/7dkj_30707.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dkj_30707/02_2024/7dkj_30707.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dkj_30707/02_2024/7dkj_30707.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dkj_30707/02_2024/7dkj_30707.pdb" } resolution = 3.7 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= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 12633 2.51 5 N 3381 2.21 5 O 3984 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 36": "OE1" <-> "OE2" Residue "A GLU 77": "OE1" <-> "OE2" Residue "A TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 83": "OE1" <-> "OE2" Residue "A ARG 88": "NH1" <-> "NH2" Residue "A GLU 114": "OE1" <-> "OE2" Residue "A ARG 134": "NH1" <-> "NH2" Residue "A GLU 213": "OE1" <-> "OE2" Residue "A GLU 228": "OE1" <-> "OE2" Residue "A GLU 252": "OE1" <-> "OE2" Residue "A TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 338": "OE1" <-> "OE2" Residue "A ASP 373": "OD1" <-> "OD2" Residue "A ASP 455": "OD1" <-> "OD2" Residue "A GLU 459": "OE1" <-> "OE2" Residue "C ARG 38": "NH1" <-> "NH2" Residue "C GLU 46": "OE1" <-> "OE2" Residue "C ASP 53": "OD1" <-> "OD2" Residue "C TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 69": "NH1" <-> "NH2" Residue "C ARG 89": "NH1" <-> "NH2" Residue "C TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 151": "OE1" <-> "OE2" Residue "D ASP 1": "OD1" <-> "OD2" Residue "D GLU 17": "OE1" <-> "OE2" Residue "D ARG 24": "NH1" <-> "NH2" Residue "D ARG 61": "NH1" <-> "NH2" Residue "E GLU 36": "OE1" <-> "OE2" Residue "E GLU 77": "OE1" <-> "OE2" Residue "E TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 83": "OE1" <-> "OE2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E GLU 114": "OE1" <-> "OE2" Residue "E ARG 134": "NH1" <-> "NH2" Residue "E GLU 213": "OE1" <-> "OE2" Residue "E GLU 228": "OE1" <-> "OE2" Residue "E GLU 252": "OE1" <-> "OE2" Residue "E TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 338": "OE1" <-> "OE2" Residue "E ASP 373": "OD1" <-> "OD2" Residue "E ASP 455": "OD1" <-> "OD2" Residue "E GLU 459": "OE1" <-> "OE2" Residue "G ARG 38": "NH1" <-> "NH2" Residue "G GLU 46": "OE1" <-> "OE2" Residue "G ASP 53": "OD1" <-> "OD2" Residue "G TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 69": "NH1" <-> "NH2" Residue "G ARG 89": "NH1" <-> "NH2" Residue "G TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 151": "OE1" <-> "OE2" Residue "H ASP 1": "OD1" <-> "OD2" Residue "H GLU 17": "OE1" <-> "OE2" Residue "H ARG 24": "NH1" <-> "NH2" Residue "H ARG 61": "NH1" <-> "NH2" Residue "I GLU 36": "OE1" <-> "OE2" Residue "I GLU 77": "OE1" <-> "OE2" Residue "I TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 83": "OE1" <-> "OE2" Residue "I ARG 88": "NH1" <-> "NH2" Residue "I GLU 114": "OE1" <-> "OE2" Residue "I ARG 134": "NH1" <-> "NH2" Residue "I GLU 213": "OE1" <-> "OE2" Residue "I GLU 228": "OE1" <-> "OE2" Residue "I GLU 252": "OE1" <-> "OE2" Residue "I TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 338": "OE1" <-> "OE2" Residue "I ASP 373": "OD1" <-> "OD2" Residue "I ASP 455": "OD1" <-> "OD2" Residue "I GLU 459": "OE1" <-> "OE2" Residue "K ARG 38": "NH1" <-> "NH2" Residue "K GLU 46": "OE1" <-> "OE2" Residue "K ASP 53": "OD1" <-> "OD2" Residue "K TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 69": "NH1" <-> "NH2" Residue "K ARG 89": "NH1" <-> "NH2" Residue "K TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 151": "OE1" <-> "OE2" Residue "L ASP 1": "OD1" <-> "OD2" Residue "L GLU 17": "OE1" <-> "OE2" Residue "L ARG 24": "NH1" <-> "NH2" Residue "L ARG 61": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20112 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3947 Classifications: {'peptide': 498} Link IDs: {'PTRANS': 19, 'TRANS': 478} Chain: "C" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1381 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 165} Chain: "D" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1256 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain: "E" Number of atoms: 3947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3947 Classifications: {'peptide': 498} Link IDs: {'PTRANS': 19, 'TRANS': 478} Chain: "G" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1381 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 165} Chain: "H" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1256 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain: "I" Number of atoms: 3947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3947 Classifications: {'peptide': 498} Link IDs: {'PTRANS': 19, 'TRANS': 478} Chain: "K" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1381 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 165} Chain: "L" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1256 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 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: "E" 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 Time building chain proxies: 10.36, per 1000 atoms: 0.52 Number of scatterers: 20112 At special positions: 0 Unit cell: (154.35, 149.94, 148.47, 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 114 16.00 O 3984 8.00 N 3381 7.00 C 12633 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS A 6 " - pdb=" SG CYS A 464 " distance=2.03 Simple disulfide: pdb=" SG CYS A 44 " - pdb=" SG CYS A 275 " distance=2.03 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 69 " distance=2.03 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 279 " - pdb=" SG CYS A 303 " distance=2.02 Simple disulfide: pdb=" SG CYS A 471 " - pdb=" SG CYS A 475 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 98 " distance=2.03 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS D 147 " distance=1.92 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 6 " - pdb=" SG CYS E 464 " distance=2.03 Simple disulfide: pdb=" SG CYS E 44 " - pdb=" SG CYS E 275 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 69 " distance=2.03 Simple disulfide: pdb=" SG CYS E 92 " - pdb=" SG CYS E 136 " distance=2.03 Simple disulfide: pdb=" SG CYS E 279 " - pdb=" SG CYS E 303 " distance=2.02 Simple disulfide: pdb=" SG CYS E 471 " - pdb=" SG CYS E 475 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 98 " distance=2.03 Simple disulfide: pdb=" SG CYS G 121 " - pdb=" SG CYS H 147 " distance=1.97 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 6 " - pdb=" SG CYS I 464 " distance=2.03 Simple disulfide: pdb=" SG CYS I 44 " - pdb=" SG CYS I 275 " distance=2.03 Simple disulfide: pdb=" SG CYS I 57 " - pdb=" SG CYS I 69 " distance=2.03 Simple disulfide: pdb=" SG CYS I 92 " - pdb=" SG CYS I 136 " distance=2.03 Simple disulfide: pdb=" SG CYS I 279 " - pdb=" SG CYS I 303 " distance=2.02 Simple disulfide: pdb=" SG CYS I 471 " - pdb=" SG CYS I 475 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 98 " distance=2.03 Simple disulfide: pdb=" SG CYS K 121 " - pdb=" SG CYS L 147 " distance=2.21 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " NAG-ASN " NAG A 601 " - " ASN A 13 " " NAG A 602 " - " ASN A 25 " " NAG A 603 " - " ASN A 287 " " NAG B 1 " - " ASN A 166 " " NAG E 601 " - " ASN E 13 " " NAG E 602 " - " ASN E 25 " " NAG E 603 " - " ASN E 287 " " NAG F 1 " - " ASN A 481 " " NAG I 601 " - " ASN I 13 " " NAG I 602 " - " ASN I 25 " " NAG I 603 " - " ASN I 287 " " NAG J 1 " - " ASN E 166 " " NAG M 1 " - " ASN E 481 " " NAG N 1 " - " ASN I 166 " " NAG O 1 " - " ASN I 481 " Time building additional restraints: 8.05 Conformation dependent library (CDL) restraints added in 3.2 seconds 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4560 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 45 sheets defined 28.1% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.07 Creating SS restraints... Processing helix chain 'A' and resid 58 through 65 Processing helix chain 'A' and resid 99 through 108 Processing helix chain 'A' and resid 184 through 193 Processing helix chain 'A' and resid 364 through 386 Processing helix chain 'A' and resid 398 through 400 No H-bonds generated for 'chain 'A' and resid 398 through 400' Processing helix chain 'A' and resid 401 through 453 removed outlier: 3.938A pdb=" N LEU A 426 " --> pdb=" O ASN A 422 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE A 437 " --> pdb=" O ARG A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 481 Processing helix chain 'A' and resid 485 through 499 removed outlier: 3.825A pdb=" N TYR A 489 " --> pdb=" O ASP A 485 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLU A 491 " --> pdb=" O PRO A 487 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N GLU A 492 " --> pdb=" O LYS A 488 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU A 499 " --> pdb=" O LEU A 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 57 removed outlier: 3.841A pdb=" N ASN C 56 " --> pdb=" O ASP C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 67 Processing helix chain 'C' and resid 76 through 78 No H-bonds generated for 'chain 'C' and resid 76 through 78' Processing helix chain 'C' and resid 89 through 93 Processing helix chain 'C' and resid 133 through 170 Proline residue: C 146 - end of helix Proline residue: C 165 - end of helix Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'D' and resid 120 through 159 removed outlier: 3.806A pdb=" N GLN D 124 " --> pdb=" O VAL D 120 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ASP D 131 " --> pdb=" O LEU D 127 " (cutoff:3.500A) Proline residue: D 132 - end of helix Proline residue: D 151 - end of helix removed outlier: 3.715A pdb=" N LYS D 159 " --> pdb=" O ALA D 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 65 Processing helix chain 'E' and resid 99 through 108 Processing helix chain 'E' and resid 184 through 193 Processing helix chain 'E' and resid 364 through 386 Processing helix chain 'E' and resid 398 through 400 No H-bonds generated for 'chain 'E' and resid 398 through 400' Processing helix chain 'E' and resid 401 through 453 removed outlier: 3.939A pdb=" N LEU E 426 " --> pdb=" O ASN E 422 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE E 437 " --> pdb=" O ARG E 433 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 481 Processing helix chain 'E' and resid 485 through 499 removed outlier: 3.824A pdb=" N TYR E 489 " --> pdb=" O ASP E 485 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLU E 491 " --> pdb=" O PRO E 487 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N GLU E 492 " --> pdb=" O LYS E 488 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU E 499 " --> pdb=" O LEU E 495 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 57 removed outlier: 3.842A pdb=" N ASN G 56 " --> pdb=" O ASP G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 67 Processing helix chain 'G' and resid 76 through 78 No H-bonds generated for 'chain 'G' and resid 76 through 78' Processing helix chain 'G' and resid 89 through 93 Processing helix chain 'G' and resid 133 through 170 Proline residue: G 146 - end of helix Proline residue: G 165 - end of helix Processing helix chain 'H' and resid 79 through 83 Processing helix chain 'H' and resid 120 through 159 removed outlier: 3.806A pdb=" N GLN H 124 " --> pdb=" O VAL H 120 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ASP H 131 " --> pdb=" O LEU H 127 " (cutoff:3.500A) Proline residue: H 132 - end of helix Proline residue: H 151 - end of helix removed outlier: 3.715A pdb=" N LYS H 159 " --> pdb=" O ALA H 155 " (cutoff:3.500A) Processing helix chain 'I' and resid 58 through 65 Processing helix chain 'I' and resid 99 through 108 Processing helix chain 'I' and resid 184 through 193 Processing helix chain 'I' and resid 364 through 386 Processing helix chain 'I' and resid 398 through 400 No H-bonds generated for 'chain 'I' and resid 398 through 400' Processing helix chain 'I' and resid 401 through 453 removed outlier: 3.938A pdb=" N LEU I 426 " --> pdb=" O ASN I 422 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE I 437 " --> pdb=" O ARG I 433 " (cutoff:3.500A) Processing helix chain 'I' and resid 472 through 481 Processing helix chain 'I' and resid 485 through 499 removed outlier: 3.825A pdb=" N TYR I 489 " --> pdb=" O ASP I 485 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLU I 491 " --> pdb=" O PRO I 487 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N GLU I 492 " --> pdb=" O LYS I 488 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU I 499 " --> pdb=" O LEU I 495 " (cutoff:3.500A) Processing helix chain 'K' and resid 53 through 57 removed outlier: 3.841A pdb=" N ASN K 56 " --> pdb=" O ASP K 53 " (cutoff:3.500A) Processing helix chain 'K' and resid 63 through 67 Processing helix chain 'K' and resid 76 through 78 No H-bonds generated for 'chain 'K' and resid 76 through 78' Processing helix chain 'K' and resid 89 through 93 Processing helix chain 'K' and resid 133 through 170 Proline residue: K 146 - end of helix Proline residue: K 165 - end of helix Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'L' and resid 120 through 159 removed outlier: 3.806A pdb=" N GLN L 124 " --> pdb=" O VAL L 120 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ASP L 131 " --> pdb=" O LEU L 127 " (cutoff:3.500A) Proline residue: L 132 - end of helix Proline residue: L 151 - end of helix removed outlier: 3.715A pdb=" N LYS L 159 " --> pdb=" O ALA L 155 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 9 Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 18 Processing sheet with id=AA3, first strand: chain 'A' and resid 32 through 33 Processing sheet with id=AA4, first strand: chain 'A' and resid 44 through 46 removed outlier: 6.599A pdb=" N LYS A 45 " --> pdb=" O THR A 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 81 through 83 removed outlier: 6.817A pdb=" N ILE A 81 " --> pdb=" O ILE A 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 112 through 117 removed outlier: 6.737A pdb=" N HIS A 112 " --> pdb=" O SER A 258 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TYR A 253 " --> pdb=" O ILE A 176 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ILE A 176 " --> pdb=" O TYR A 253 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ILE A 176 " --> pdb=" O PRO A 251 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 112 through 117 removed outlier: 6.737A pdb=" N HIS A 112 " --> pdb=" O SER A 258 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TYR A 253 " --> pdb=" O ILE A 176 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ILE A 176 " --> pdb=" O TYR A 253 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 161 through 165 Processing sheet with id=AA9, first strand: chain 'A' and resid 292 through 293 Processing sheet with id=AB1, first strand: chain 'A' and resid 457 through 458 Processing sheet with id=AB2, first strand: chain 'C' and resid 4 through 7 removed outlier: 4.026A pdb=" N ILE C 80 " --> pdb=" O ASP C 75 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 46 through 51 removed outlier: 6.608A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N MET C 34 " --> pdb=" O PHE C 50 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N CYS C 98 " --> pdb=" O TRP C 112 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N TRP C 112 " --> pdb=" O CYS C 98 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ARG C 100 " --> pdb=" O ASP C 110 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 46 through 51 removed outlier: 6.608A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N MET C 34 " --> pdb=" O PHE C 50 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 19 through 24 Processing sheet with id=AB6, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AB7, first strand: chain 'E' and resid 5 through 9 Processing sheet with id=AB8, first strand: chain 'E' and resid 17 through 18 Processing sheet with id=AB9, first strand: chain 'E' and resid 32 through 33 Processing sheet with id=AC1, first strand: chain 'E' and resid 44 through 46 removed outlier: 6.599A pdb=" N LYS E 45 " --> pdb=" O THR E 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'E' and resid 81 through 83 removed outlier: 6.819A pdb=" N ILE E 81 " --> pdb=" O ILE E 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'E' and resid 112 through 117 removed outlier: 6.738A pdb=" N HIS E 112 " --> pdb=" O SER E 258 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N TYR E 253 " --> pdb=" O ILE E 176 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ILE E 176 " --> pdb=" O TYR E 253 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ILE E 176 " --> pdb=" O PRO E 251 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 112 through 117 removed outlier: 6.738A pdb=" N HIS E 112 " --> pdb=" O SER E 258 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N TYR E 253 " --> pdb=" O ILE E 176 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ILE E 176 " --> pdb=" O TYR E 253 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 161 through 165 Processing sheet with id=AC6, first strand: chain 'E' and resid 292 through 293 Processing sheet with id=AC7, first strand: chain 'E' and resid 457 through 458 Processing sheet with id=AC8, first strand: chain 'G' and resid 4 through 7 removed outlier: 4.025A pdb=" N ILE G 80 " --> pdb=" O ASP G 75 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 46 through 51 removed outlier: 6.609A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N MET G 34 " --> pdb=" O PHE G 50 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N CYS G 98 " --> pdb=" O TRP G 112 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N TRP G 112 " --> pdb=" O CYS G 98 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ARG G 100 " --> pdb=" O ASP G 110 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 46 through 51 removed outlier: 6.609A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N MET G 34 " --> pdb=" O PHE G 50 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 19 through 24 Processing sheet with id=AD3, first strand: chain 'H' and resid 53 through 54 Processing sheet with id=AD4, first strand: chain 'I' and resid 5 through 9 Processing sheet with id=AD5, first strand: chain 'I' and resid 17 through 18 Processing sheet with id=AD6, first strand: chain 'I' and resid 32 through 33 Processing sheet with id=AD7, first strand: chain 'I' and resid 44 through 46 removed outlier: 6.599A pdb=" N LYS I 45 " --> pdb=" O THR I 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'I' and resid 81 through 83 removed outlier: 6.818A pdb=" N ILE I 81 " --> pdb=" O ILE I 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'I' and resid 112 through 117 removed outlier: 6.738A pdb=" N HIS I 112 " --> pdb=" O SER I 258 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TYR I 253 " --> pdb=" O ILE I 176 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ILE I 176 " --> pdb=" O TYR I 253 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ILE I 176 " --> pdb=" O PRO I 251 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 112 through 117 removed outlier: 6.738A pdb=" N HIS I 112 " --> pdb=" O SER I 258 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TYR I 253 " --> pdb=" O ILE I 176 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ILE I 176 " --> pdb=" O TYR I 253 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 161 through 165 Processing sheet with id=AE3, first strand: chain 'I' and resid 292 through 293 Processing sheet with id=AE4, first strand: chain 'I' and resid 457 through 458 Processing sheet with id=AE5, first strand: chain 'K' and resid 4 through 7 removed outlier: 4.025A pdb=" N ILE K 80 " --> pdb=" O ASP K 75 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 46 through 51 removed outlier: 6.608A pdb=" N TRP K 36 " --> pdb=" O LEU K 48 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N MET K 34 " --> pdb=" O PHE K 50 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N CYS K 98 " --> pdb=" O TRP K 112 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N TRP K 112 " --> pdb=" O CYS K 98 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ARG K 100 " --> pdb=" O ASP K 110 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 46 through 51 removed outlier: 6.608A pdb=" N TRP K 36 " --> pdb=" O LEU K 48 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N MET K 34 " --> pdb=" O PHE K 50 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AE9, first strand: chain 'L' and resid 53 through 54 822 hydrogen bonds defined for protein. 2232 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: 6.43 Time building geometry restraints manager: 8.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6501 1.34 - 1.46: 4648 1.46 - 1.58: 9233 1.58 - 1.70: 0 1.70 - 1.82: 168 Bond restraints: 20550 Sorted by residual: bond pdb=" C1 BMA O 3 " pdb=" C2 BMA O 3 " ideal model delta sigma weight residual 1.519 1.571 -0.052 2.00e-02 2.50e+03 6.72e+00 bond pdb=" C1 BMA F 3 " pdb=" C2 BMA F 3 " ideal model delta sigma weight residual 1.519 1.571 -0.052 2.00e-02 2.50e+03 6.63e+00 bond pdb=" C1 BMA M 3 " pdb=" C2 BMA M 3 " ideal model delta sigma weight residual 1.519 1.570 -0.051 2.00e-02 2.50e+03 6.62e+00 bond pdb=" CG1 ILE A 383 " pdb=" CD1 ILE A 383 " ideal model delta sigma weight residual 1.513 1.415 0.098 3.90e-02 6.57e+02 6.29e+00 bond pdb=" CG1 ILE E 383 " pdb=" CD1 ILE E 383 " ideal model delta sigma weight residual 1.513 1.415 0.098 3.90e-02 6.57e+02 6.25e+00 ... (remaining 20545 not shown) Histogram of bond angle deviations from ideal: 98.40 - 105.53: 337 105.53 - 112.65: 10725 112.65 - 119.77: 6880 119.77 - 126.89: 9576 126.89 - 134.01: 277 Bond angle restraints: 27795 Sorted by residual: angle pdb=" CA GLN K 78 " pdb=" CB GLN K 78 " pdb=" CG GLN K 78 " ideal model delta sigma weight residual 114.10 124.54 -10.44 2.00e+00 2.50e-01 2.72e+01 angle pdb=" CA GLN C 78 " pdb=" CB GLN C 78 " pdb=" CG GLN C 78 " ideal model delta sigma weight residual 114.10 124.53 -10.43 2.00e+00 2.50e-01 2.72e+01 angle pdb=" CA GLN G 78 " pdb=" CB GLN G 78 " pdb=" CG GLN G 78 " ideal model delta sigma weight residual 114.10 124.52 -10.42 2.00e+00 2.50e-01 2.71e+01 angle pdb=" CB GLN C 78 " pdb=" CG GLN C 78 " pdb=" CD GLN C 78 " ideal model delta sigma weight residual 112.60 118.99 -6.39 1.70e+00 3.46e-01 1.41e+01 angle pdb=" CB GLN K 78 " pdb=" CG GLN K 78 " pdb=" CD GLN K 78 " ideal model delta sigma weight residual 112.60 118.99 -6.39 1.70e+00 3.46e-01 1.41e+01 ... (remaining 27790 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.28: 11331 21.28 - 42.56: 955 42.56 - 63.84: 172 63.84 - 85.11: 119 85.11 - 106.39: 104 Dihedral angle restraints: 12681 sinusoidal: 5529 harmonic: 7152 Sorted by residual: dihedral pdb=" CB CYS E 44 " pdb=" SG CYS E 44 " pdb=" SG CYS E 275 " pdb=" CB CYS E 275 " ideal model delta sinusoidal sigma weight residual -86.00 -9.61 -76.39 1 1.00e+01 1.00e-02 7.34e+01 dihedral pdb=" CB CYS I 44 " pdb=" SG CYS I 44 " pdb=" SG CYS I 275 " pdb=" CB CYS I 275 " ideal model delta sinusoidal sigma weight residual -86.00 -9.62 -76.38 1 1.00e+01 1.00e-02 7.34e+01 dihedral pdb=" CB CYS A 44 " pdb=" SG CYS A 44 " pdb=" SG CYS A 275 " pdb=" CB CYS A 275 " ideal model delta sinusoidal sigma weight residual -86.00 -9.64 -76.36 1 1.00e+01 1.00e-02 7.34e+01 ... (remaining 12678 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 2846 0.097 - 0.194: 190 0.194 - 0.291: 9 0.291 - 0.387: 0 0.387 - 0.484: 3 Chirality restraints: 3048 Sorted by residual: chirality pdb=" C1 NAG I 602 " pdb=" ND2 ASN I 25 " pdb=" C2 NAG I 602 " pdb=" O5 NAG I 602 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.87e+00 chirality pdb=" C1 NAG E 602 " pdb=" ND2 ASN E 25 " pdb=" C2 NAG E 602 " pdb=" O5 NAG E 602 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.79e+00 chirality pdb=" C1 NAG A 602 " pdb=" ND2 ASN A 25 " pdb=" C2 NAG A 602 " pdb=" O5 NAG A 602 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.78e+00 ... (remaining 3045 not shown) Planarity restraints: 3582 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 94 " -0.047 5.00e-02 4.00e+02 7.16e-02 8.19e+00 pdb=" N PRO D 95 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO D 95 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 95 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR L 94 " -0.047 5.00e-02 4.00e+02 7.14e-02 8.15e+00 pdb=" N PRO L 95 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO L 95 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO L 95 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR H 94 " 0.047 5.00e-02 4.00e+02 7.12e-02 8.12e+00 pdb=" N PRO H 95 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO H 95 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO H 95 " 0.040 5.00e-02 4.00e+02 ... (remaining 3579 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.62: 348 2.62 - 3.19: 19418 3.19 - 3.76: 31253 3.76 - 4.33: 43362 4.33 - 4.90: 71032 Nonbonded interactions: 165413 Sorted by model distance: nonbonded pdb=" OG1 THR E 128 " pdb=" OG1 THR E 152 " model vdw 2.056 2.440 nonbonded pdb=" OG1 THR A 128 " pdb=" OG1 THR A 152 " model vdw 2.056 2.440 nonbonded pdb=" OG1 THR I 128 " pdb=" OG1 THR I 152 " model vdw 2.056 2.440 nonbonded pdb=" NZ LYS L 39 " pdb=" O GLU L 81 " model vdw 2.090 2.520 nonbonded pdb=" NZ LYS D 39 " pdb=" O GLU D 81 " model vdw 2.090 2.520 ... (remaining 165408 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 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' selection = chain 'M' selection = chain 'N' selection = chain 'O' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.190 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: 2.050 Check model and map are aligned: 0.290 Set scattering table: 0.170 Process input model: 51.340 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.170 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 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 0.098 20550 Z= 0.485 Angle : 0.873 10.440 27795 Z= 0.463 Chirality : 0.054 0.484 3048 Planarity : 0.005 0.072 3567 Dihedral : 20.249 106.392 8040 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 1.84 % Allowed : 2.26 % Favored : 95.90 % 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: -2.34 (0.16), residues: 2472 helix: -1.01 (0.20), residues: 597 sheet: -1.31 (0.22), residues: 567 loop : -1.91 (0.16), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP I 150 HIS 0.005 0.001 HIS I 10 PHE 0.015 0.002 PHE I 229 TYR 0.023 0.002 TYR L 145 ARG 0.012 0.002 ARG K 54 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 418 time to evaluate : 2.132 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: symmetry clash REVERT: A 21 ILE cc_start: 0.8316 (OUTLIER) cc_final: 0.7848 (tp) REVERT: A 337 ILE cc_start: 0.8898 (mm) cc_final: 0.8591 (mm) REVERT: A 411 MET cc_start: 0.8349 (tmm) cc_final: 0.7653 (tmm) REVERT: A 412 GLU cc_start: 0.7140 (tt0) cc_final: 0.6598 (tt0) REVERT: A 433 ARG cc_start: 0.7001 (OUTLIER) cc_final: 0.5783 (mmt-90) REVERT: A 451 MET cc_start: 0.8506 (ttm) cc_final: 0.8280 (ttm) REVERT: C 78 GLN cc_start: 0.5983 (OUTLIER) cc_final: 0.4934 (pt0) REVERT: C 96 TYR cc_start: 0.7132 (m-80) cc_final: 0.6758 (m-80) REVERT: C 109 MET cc_start: 0.8181 (mmm) cc_final: 0.7926 (mmm) REVERT: D 145 TYR cc_start: 0.4520 (OUTLIER) cc_final: 0.3807 (m-10) REVERT: E 21 ILE cc_start: 0.8495 (OUTLIER) cc_final: 0.8198 (tp) REVERT: E 93 PHE cc_start: 0.7461 (t80) cc_final: 0.7185 (t80) REVERT: E 175 ILE cc_start: 0.9200 (mm) cc_final: 0.8904 (mm) REVERT: E 236 MET cc_start: 0.6893 (OUTLIER) cc_final: 0.6507 (mmp) REVERT: E 260 ARG cc_start: 0.7827 (mmm160) cc_final: 0.7511 (mmp80) REVERT: E 271 THR cc_start: 0.8401 (t) cc_final: 0.8098 (m) REVERT: E 308 LYS cc_start: 0.8300 (mtpp) cc_final: 0.7951 (mttm) REVERT: E 324 ILE cc_start: 0.6598 (OUTLIER) cc_final: 0.6381 (pt) REVERT: E 337 ILE cc_start: 0.9031 (mm) cc_final: 0.8701 (mm) REVERT: E 341 TRP cc_start: 0.8748 (m-10) cc_final: 0.8383 (m-10) REVERT: E 411 MET cc_start: 0.8436 (tmm) cc_final: 0.7977 (tmm) REVERT: E 412 GLU cc_start: 0.7038 (tt0) cc_final: 0.6689 (mt-10) REVERT: E 468 TYR cc_start: 0.7936 (m-80) cc_final: 0.7404 (m-80) REVERT: G 12 VAL cc_start: 0.8499 (t) cc_final: 0.8078 (m) REVERT: G 31 ASP cc_start: 0.7817 (p0) cc_final: 0.7576 (p0) REVERT: G 33 TYR cc_start: 0.7753 (m-80) cc_final: 0.7549 (m-10) REVERT: G 34 MET cc_start: 0.6892 (tpp) cc_final: 0.6675 (tpt) REVERT: G 35 THR cc_start: 0.7670 (m) cc_final: 0.7402 (m) REVERT: G 71 THR cc_start: 0.7846 (p) cc_final: 0.7620 (p) REVERT: G 73 SER cc_start: 0.7804 (OUTLIER) cc_final: 0.7499 (m) REVERT: G 78 GLN cc_start: 0.5270 (OUTLIER) cc_final: 0.4974 (mp10) REVERT: G 109 MET cc_start: 0.7563 (mmm) cc_final: 0.7233 (mmm) REVERT: H 145 TYR cc_start: 0.4181 (OUTLIER) cc_final: 0.3332 (m-80) REVERT: I 83 GLU cc_start: 0.7409 (tt0) cc_final: 0.6882 (tt0) REVERT: I 93 PHE cc_start: 0.7395 (t80) cc_final: 0.7133 (t80) REVERT: I 146 ARG cc_start: 0.6687 (mpt180) cc_final: 0.6477 (mmt-90) REVERT: I 236 MET cc_start: 0.7257 (OUTLIER) cc_final: 0.6998 (mmp) REVERT: I 308 LYS cc_start: 0.8542 (mtpp) cc_final: 0.8271 (mttp) REVERT: I 324 ILE cc_start: 0.7696 (OUTLIER) cc_final: 0.7451 (pt) REVERT: I 355 ASN cc_start: 0.8739 (t0) cc_final: 0.8458 (t0) REVERT: I 468 TYR cc_start: 0.8669 (m-80) cc_final: 0.8448 (m-80) REVERT: K 12 VAL cc_start: 0.7479 (t) cc_final: 0.7190 (m) REVERT: K 13 GLN cc_start: 0.7329 (mm110) cc_final: 0.7092 (mm110) REVERT: K 73 SER cc_start: 0.7557 (OUTLIER) cc_final: 0.7345 (m) REVERT: K 109 MET cc_start: 0.7504 (mmm) cc_final: 0.7156 (mmm) REVERT: K 149 GLU cc_start: 0.4278 (mp0) cc_final: 0.3895 (mm-30) REVERT: L 145 TYR cc_start: 0.4942 (OUTLIER) cc_final: 0.3674 (m-80) outliers start: 40 outliers final: 7 residues processed: 444 average time/residue: 0.3082 time to fit residues: 207.4975 Evaluate side-chains 342 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 321 time to evaluate : 2.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 433 ARG Chi-restraints excluded: chain C residue 78 GLN Chi-restraints excluded: chain D residue 74 LYS Chi-restraints excluded: chain D residue 145 TYR Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 236 MET Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 433 ARG Chi-restraints excluded: chain G residue 73 SER Chi-restraints excluded: chain G residue 78 GLN Chi-restraints excluded: chain H residue 145 TYR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 236 MET Chi-restraints excluded: chain I residue 324 ILE Chi-restraints excluded: chain I residue 433 ARG Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain L residue 145 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 0.8980 chunk 184 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 62 optimal weight: 30.0000 chunk 124 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 190 optimal weight: 0.9980 chunk 73 optimal weight: 8.9990 chunk 115 optimal weight: 2.9990 chunk 141 optimal weight: 7.9990 chunk 220 optimal weight: 0.7980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 ASN ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 GLN A 353 HIS C 13 GLN ** C 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 ASN ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 GLN E 353 HIS ** E 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 377 ASN E 408 ASN E 477 ASN ** G 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 136 GLN H 146 GLN I 194 ASN ** I 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 280 GLN I 377 ASN ** K 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 20550 Z= 0.231 Angle : 0.705 8.538 27795 Z= 0.359 Chirality : 0.048 0.409 3048 Planarity : 0.005 0.054 3567 Dihedral : 15.284 84.146 3304 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.44 % Allowed : 10.56 % Favored : 87.00 % 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: -1.56 (0.16), residues: 2472 helix: 0.68 (0.22), residues: 594 sheet: -1.28 (0.21), residues: 564 loop : -1.76 (0.16), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 150 HIS 0.012 0.001 HIS A 353 PHE 0.012 0.002 PHE I 372 TYR 0.020 0.002 TYR K 82 ARG 0.006 0.001 ARG I 260 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 344 time to evaluate : 2.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ILE cc_start: 0.8016 (mm) cc_final: 0.7693 (tp) REVERT: A 36 GLU cc_start: 0.7055 (tp30) cc_final: 0.6801 (tp30) REVERT: A 236 MET cc_start: 0.7736 (mmt) cc_final: 0.7531 (mmt) REVERT: A 337 ILE cc_start: 0.8977 (mm) cc_final: 0.8617 (mm) REVERT: A 411 MET cc_start: 0.8792 (tmm) cc_final: 0.8336 (tmm) REVERT: A 412 GLU cc_start: 0.7159 (tt0) cc_final: 0.6489 (mt-10) REVERT: A 433 ARG cc_start: 0.7312 (OUTLIER) cc_final: 0.6117 (mmt90) REVERT: C 62 TYR cc_start: 0.8102 (m-80) cc_final: 0.7662 (m-80) REVERT: C 78 GLN cc_start: 0.5599 (mp10) cc_final: 0.5196 (pt0) REVERT: C 110 ASP cc_start: 0.8433 (p0) cc_final: 0.8066 (p0) REVERT: C 144 LEU cc_start: 0.4843 (tt) cc_final: 0.4557 (mp) REVERT: E 115 LYS cc_start: 0.7426 (ttmt) cc_final: 0.6877 (ttmt) REVERT: E 191 LEU cc_start: 0.8050 (mt) cc_final: 0.7305 (mt) REVERT: E 271 THR cc_start: 0.8507 (t) cc_final: 0.8124 (m) REVERT: E 308 LYS cc_start: 0.8302 (mtpp) cc_final: 0.8027 (mttm) REVERT: E 324 ILE cc_start: 0.6468 (OUTLIER) cc_final: 0.6214 (pt) REVERT: E 337 ILE cc_start: 0.9039 (mm) cc_final: 0.8728 (mm) REVERT: E 341 TRP cc_start: 0.8616 (m-10) cc_final: 0.8283 (m-10) REVERT: E 353 HIS cc_start: 0.6615 (OUTLIER) cc_final: 0.6406 (p-80) REVERT: E 411 MET cc_start: 0.8791 (tmm) cc_final: 0.8450 (tmm) REVERT: E 412 GLU cc_start: 0.6930 (tt0) cc_final: 0.6646 (mt-10) REVERT: E 433 ARG cc_start: 0.7362 (OUTLIER) cc_final: 0.6477 (mmp80) REVERT: E 466 GLU cc_start: 0.7958 (tt0) cc_final: 0.7677 (tt0) REVERT: E 468 TYR cc_start: 0.7981 (m-80) cc_final: 0.7550 (m-80) REVERT: G 12 VAL cc_start: 0.8436 (t) cc_final: 0.7966 (m) REVERT: G 34 MET cc_start: 0.7783 (tpp) cc_final: 0.7579 (mmm) REVERT: G 47 TRP cc_start: 0.8171 (t60) cc_final: 0.7966 (t60) REVERT: G 70 PHE cc_start: 0.7485 (m-10) cc_final: 0.7251 (m-10) REVERT: G 149 GLU cc_start: 0.2170 (mp0) cc_final: 0.1782 (mm-30) REVERT: H 133 MET cc_start: 0.2154 (ppp) cc_final: 0.0812 (tpt) REVERT: I 83 GLU cc_start: 0.7402 (tt0) cc_final: 0.6956 (tt0) REVERT: I 115 LYS cc_start: 0.8304 (ttpp) cc_final: 0.8015 (ttpp) REVERT: I 308 LYS cc_start: 0.8530 (mtpp) cc_final: 0.8261 (mttp) REVERT: I 324 ILE cc_start: 0.7720 (OUTLIER) cc_final: 0.7442 (pt) REVERT: I 337 ILE cc_start: 0.9171 (mm) cc_final: 0.8749 (mm) REVERT: I 433 ARG cc_start: 0.7168 (OUTLIER) cc_final: 0.6246 (mmp-170) REVERT: I 466 GLU cc_start: 0.7907 (tt0) cc_final: 0.7446 (tm-30) REVERT: I 486 TYR cc_start: 0.8073 (t80) cc_final: 0.7678 (t80) REVERT: K 12 VAL cc_start: 0.7497 (t) cc_final: 0.7261 (m) REVERT: K 13 GLN cc_start: 0.7307 (mm110) cc_final: 0.7056 (mm110) REVERT: K 78 GLN cc_start: 0.5081 (mp10) cc_final: 0.4787 (pt0) REVERT: K 109 MET cc_start: 0.7633 (mmm) cc_final: 0.7391 (mmm) REVERT: K 110 ASP cc_start: 0.8393 (p0) cc_final: 0.8154 (p0) REVERT: L 22 THR cc_start: 0.7954 (OUTLIER) cc_final: 0.7637 (p) REVERT: L 134 MET cc_start: 0.2412 (mtp) cc_final: 0.1304 (mtp) outliers start: 53 outliers final: 28 residues processed: 373 average time/residue: 0.3129 time to fit residues: 179.3699 Evaluate side-chains 344 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 309 time to evaluate : 2.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 433 ARG Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 74 LYS Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 353 HIS Chi-restraints excluded: chain E residue 433 ARG Chi-restraints excluded: chain G residue 56 ASN Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 134 MET Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 204 SER Chi-restraints excluded: chain I residue 239 THR Chi-restraints excluded: chain I residue 262 SER Chi-restraints excluded: chain I residue 299 THR Chi-restraints excluded: chain I residue 324 ILE Chi-restraints excluded: chain I residue 433 ARG Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 75 ASP Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 22 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 122 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 chunk 183 optimal weight: 7.9990 chunk 150 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 221 optimal weight: 0.0870 chunk 238 optimal weight: 0.9990 chunk 196 optimal weight: 2.9990 chunk 219 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 177 optimal weight: 4.9990 overall best weight: 1.0762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 ASN C 157 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 353 HIS E 377 ASN G 157 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 353 HIS I 477 ASN K 157 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 20550 Z= 0.199 Angle : 0.639 8.433 27795 Z= 0.321 Chirality : 0.047 0.382 3048 Planarity : 0.004 0.059 3567 Dihedral : 11.427 72.673 3277 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.67 % Allowed : 12.68 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.17), residues: 2472 helix: 1.20 (0.22), residues: 594 sheet: -1.05 (0.22), residues: 528 loop : -1.64 (0.16), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP I 150 HIS 0.017 0.001 HIS E 353 PHE 0.011 0.001 PHE E 93 TYR 0.020 0.002 TYR I 468 ARG 0.005 0.000 ARG K 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 339 time to evaluate : 2.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ILE cc_start: 0.7940 (mm) cc_final: 0.7718 (tp) REVERT: A 36 GLU cc_start: 0.7021 (tp30) cc_final: 0.6772 (tp30) REVERT: A 236 MET cc_start: 0.7689 (mmt) cc_final: 0.7464 (mmt) REVERT: A 337 ILE cc_start: 0.9006 (mm) cc_final: 0.8632 (mm) REVERT: A 411 MET cc_start: 0.8996 (tmm) cc_final: 0.8509 (tmm) REVERT: A 412 GLU cc_start: 0.7176 (tt0) cc_final: 0.6547 (mt-10) REVERT: A 433 ARG cc_start: 0.7189 (OUTLIER) cc_final: 0.6361 (mtt-85) REVERT: A 468 TYR cc_start: 0.8498 (m-80) cc_final: 0.8274 (m-80) REVERT: C 62 TYR cc_start: 0.8133 (m-80) cc_final: 0.7729 (m-80) REVERT: C 78 GLN cc_start: 0.6035 (mp10) cc_final: 0.5435 (pt0) REVERT: C 144 LEU cc_start: 0.5168 (tt) cc_final: 0.4867 (mp) REVERT: E 271 THR cc_start: 0.8424 (t) cc_final: 0.8155 (m) REVERT: E 308 LYS cc_start: 0.8453 (mtpp) cc_final: 0.8226 (tttt) REVERT: E 324 ILE cc_start: 0.6650 (OUTLIER) cc_final: 0.6411 (pt) REVERT: E 337 ILE cc_start: 0.9123 (mm) cc_final: 0.8859 (mm) REVERT: E 341 TRP cc_start: 0.8582 (m-10) cc_final: 0.8231 (m-10) REVERT: E 411 MET cc_start: 0.8782 (tmm) cc_final: 0.8504 (tmm) REVERT: E 412 GLU cc_start: 0.6995 (tt0) cc_final: 0.6738 (mt-10) REVERT: E 429 MET cc_start: 0.7334 (mtp) cc_final: 0.7107 (mtt) REVERT: E 433 ARG cc_start: 0.7116 (OUTLIER) cc_final: 0.6250 (tpt-90) REVERT: E 466 GLU cc_start: 0.7907 (tt0) cc_final: 0.7566 (tt0) REVERT: E 468 TYR cc_start: 0.7912 (m-80) cc_final: 0.7435 (m-80) REVERT: G 12 VAL cc_start: 0.8300 (t) cc_final: 0.7966 (m) REVERT: G 47 TRP cc_start: 0.8023 (t60) cc_final: 0.7733 (t60) REVERT: G 82 TYR cc_start: 0.5647 (m-80) cc_final: 0.5198 (m-80) REVERT: G 149 GLU cc_start: 0.2745 (mp0) cc_final: 0.1848 (mm-30) REVERT: I 83 GLU cc_start: 0.7321 (tt0) cc_final: 0.6805 (tt0) REVERT: I 84 LYS cc_start: 0.8054 (mtpp) cc_final: 0.7725 (mtmm) REVERT: I 115 LYS cc_start: 0.8226 (ttpp) cc_final: 0.7837 (ttmm) REVERT: I 308 LYS cc_start: 0.8518 (mtpp) cc_final: 0.8286 (mttp) REVERT: I 324 ILE cc_start: 0.7589 (OUTLIER) cc_final: 0.7255 (pt) REVERT: I 337 ILE cc_start: 0.9153 (mm) cc_final: 0.8756 (mm) REVERT: I 433 ARG cc_start: 0.7217 (OUTLIER) cc_final: 0.6625 (tpt-90) REVERT: I 466 GLU cc_start: 0.7889 (tt0) cc_final: 0.7456 (tm-30) REVERT: K 109 MET cc_start: 0.7521 (mmm) cc_final: 0.7258 (mmm) REVERT: L 22 THR cc_start: 0.7941 (OUTLIER) cc_final: 0.7615 (p) outliers start: 58 outliers final: 33 residues processed: 368 average time/residue: 0.3104 time to fit residues: 176.1153 Evaluate side-chains 338 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 299 time to evaluate : 1.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 433 ARG Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 74 LYS Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 433 ARG Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 56 ASN Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 134 MET Chi-restraints excluded: chain I residue 239 THR Chi-restraints excluded: chain I residue 278 LYS Chi-restraints excluded: chain I residue 299 THR Chi-restraints excluded: chain I residue 324 ILE Chi-restraints excluded: chain I residue 353 HIS Chi-restraints excluded: chain I residue 433 ARG Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 75 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 22 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 218 optimal weight: 20.0000 chunk 166 optimal weight: 0.0470 chunk 114 optimal weight: 7.9990 chunk 24 optimal weight: 8.9990 chunk 105 optimal weight: 6.9990 chunk 148 optimal weight: 7.9990 chunk 221 optimal weight: 1.9990 chunk 234 optimal weight: 20.0000 chunk 115 optimal weight: 6.9990 chunk 210 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 overall best weight: 4.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 ASN D 79 GLN ** E 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 241 ASN E 377 ASN E 469 HIS E 477 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 352 HIS K 78 GLN L 79 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 20550 Z= 0.418 Angle : 0.741 9.110 27795 Z= 0.376 Chirality : 0.049 0.418 3048 Planarity : 0.005 0.058 3567 Dihedral : 9.809 59.510 3277 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 3.27 % Allowed : 16.74 % Favored : 79.99 % 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: -1.40 (0.16), residues: 2472 helix: 0.93 (0.21), residues: 597 sheet: -1.22 (0.22), residues: 543 loop : -1.70 (0.16), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 150 HIS 0.031 0.002 HIS I 353 PHE 0.017 0.003 PHE I 372 TYR 0.025 0.002 TYR C 82 ARG 0.007 0.001 ARG A 88 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 318 time to evaluate : 2.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 MET cc_start: 0.7925 (mmt) cc_final: 0.7689 (mmt) REVERT: A 260 ARG cc_start: 0.7862 (tpp-160) cc_final: 0.7489 (tpp-160) REVERT: A 337 ILE cc_start: 0.9041 (mm) cc_final: 0.8671 (mm) REVERT: A 411 MET cc_start: 0.8988 (tmm) cc_final: 0.8479 (tmm) REVERT: A 433 ARG cc_start: 0.7441 (OUTLIER) cc_final: 0.6415 (mtt-85) REVERT: C 31 ASP cc_start: 0.7866 (p0) cc_final: 0.7548 (p0) REVERT: C 78 GLN cc_start: 0.5929 (mp10) cc_final: 0.5344 (pt0) REVERT: C 144 LEU cc_start: 0.5153 (tt) cc_final: 0.4844 (mp) REVERT: E 115 LYS cc_start: 0.7515 (ttmt) cc_final: 0.7144 (ttmt) REVERT: E 308 LYS cc_start: 0.8634 (mtpp) cc_final: 0.8313 (mttt) REVERT: E 411 MET cc_start: 0.8791 (tmm) cc_final: 0.8498 (tmm) REVERT: E 433 ARG cc_start: 0.7006 (OUTLIER) cc_final: 0.6234 (tpt170) REVERT: E 466 GLU cc_start: 0.7908 (tt0) cc_final: 0.7606 (tt0) REVERT: E 468 TYR cc_start: 0.8118 (m-80) cc_final: 0.7539 (m-80) REVERT: G 6 GLU cc_start: 0.6626 (OUTLIER) cc_final: 0.6379 (pt0) REVERT: G 12 VAL cc_start: 0.8331 (t) cc_final: 0.7981 (m) REVERT: G 70 PHE cc_start: 0.7436 (m-10) cc_final: 0.7201 (m-10) REVERT: I 43 LEU cc_start: 0.7427 (mm) cc_final: 0.7050 (mt) REVERT: I 83 GLU cc_start: 0.7358 (tt0) cc_final: 0.7069 (tt0) REVERT: I 308 LYS cc_start: 0.8632 (mtpp) cc_final: 0.8396 (mttp) REVERT: I 324 ILE cc_start: 0.7672 (mt) cc_final: 0.7214 (pt) REVERT: I 355 ASN cc_start: 0.8462 (t0) cc_final: 0.8188 (t0) REVERT: I 429 MET cc_start: 0.7799 (mtt) cc_final: 0.7549 (mtt) REVERT: I 433 ARG cc_start: 0.7403 (OUTLIER) cc_final: 0.6910 (tpt170) REVERT: I 486 TYR cc_start: 0.8172 (t80) cc_final: 0.7950 (t80) REVERT: K 19 ARG cc_start: 0.6927 (ttm-80) cc_final: 0.6673 (ttm-80) REVERT: K 109 MET cc_start: 0.7675 (mmm) cc_final: 0.7292 (mmm) REVERT: L 74 LYS cc_start: 0.7174 (mtmm) cc_final: 0.6577 (mtmt) REVERT: L 91 PHE cc_start: 0.8327 (OUTLIER) cc_final: 0.7781 (m-10) outliers start: 71 outliers final: 49 residues processed: 365 average time/residue: 0.3113 time to fit residues: 175.6815 Evaluate side-chains 340 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 286 time to evaluate : 2.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 433 ARG Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 74 LYS Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain E residue 278 LYS Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 433 ARG Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 32 ASN Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 134 MET Chi-restraints excluded: chain I residue 148 MET Chi-restraints excluded: chain I residue 239 THR Chi-restraints excluded: chain I residue 262 SER Chi-restraints excluded: chain I residue 271 THR Chi-restraints excluded: chain I residue 278 LYS Chi-restraints excluded: chain I residue 299 THR Chi-restraints excluded: chain I residue 393 VAL Chi-restraints excluded: chain I residue 433 ARG Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 75 ASP Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 91 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 195 optimal weight: 4.9990 chunk 133 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 174 optimal weight: 9.9990 chunk 96 optimal weight: 0.8980 chunk 200 optimal weight: 6.9990 chunk 162 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 119 optimal weight: 0.0770 chunk 210 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 overall best weight: 1.3342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 377 ASN ** E 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 477 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 353 HIS ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 20550 Z= 0.202 Angle : 0.633 12.625 27795 Z= 0.317 Chirality : 0.046 0.394 3048 Planarity : 0.004 0.062 3567 Dihedral : 8.653 54.245 3273 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.67 % Allowed : 18.67 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.17), residues: 2472 helix: 1.25 (0.21), residues: 597 sheet: -1.23 (0.22), residues: 549 loop : -1.61 (0.16), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP I 150 HIS 0.015 0.001 HIS E 353 PHE 0.013 0.001 PHE I 372 TYR 0.027 0.002 TYR C 82 ARG 0.007 0.000 ARG A 88 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 312 time to evaluate : 2.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ARG cc_start: 0.4795 (mtm110) cc_final: 0.4362 (mtm110) REVERT: A 337 ILE cc_start: 0.9013 (mm) cc_final: 0.8649 (mm) REVERT: A 411 MET cc_start: 0.9016 (tmm) cc_final: 0.8269 (tmm) REVERT: A 433 ARG cc_start: 0.7467 (OUTLIER) cc_final: 0.6991 (mmp80) REVERT: C 31 ASP cc_start: 0.7831 (p0) cc_final: 0.7489 (p0) REVERT: C 78 GLN cc_start: 0.5741 (mp10) cc_final: 0.5413 (pt0) REVERT: C 144 LEU cc_start: 0.5114 (tt) cc_final: 0.4856 (mp) REVERT: D 74 LYS cc_start: 0.7465 (OUTLIER) cc_final: 0.6733 (mmtt) REVERT: E 115 LYS cc_start: 0.7441 (ttmt) cc_final: 0.6939 (ttmt) REVERT: E 308 LYS cc_start: 0.8624 (mtpp) cc_final: 0.8299 (mttt) REVERT: E 324 ILE cc_start: 0.7090 (mt) cc_final: 0.6714 (pt) REVERT: E 429 MET cc_start: 0.7505 (mtp) cc_final: 0.7276 (mtt) REVERT: E 433 ARG cc_start: 0.6963 (OUTLIER) cc_final: 0.5593 (mtt-85) REVERT: G 12 VAL cc_start: 0.8115 (t) cc_final: 0.7746 (m) REVERT: G 148 MET cc_start: 0.4201 (ttp) cc_final: 0.3984 (ttp) REVERT: I 83 GLU cc_start: 0.7326 (tt0) cc_final: 0.7040 (tt0) REVERT: I 298 LEU cc_start: 0.8815 (mt) cc_final: 0.8525 (mp) REVERT: I 308 LYS cc_start: 0.8521 (mtpp) cc_final: 0.8291 (mttp) REVERT: I 324 ILE cc_start: 0.7615 (mt) cc_final: 0.7227 (pt) REVERT: I 355 ASN cc_start: 0.8311 (t0) cc_final: 0.8096 (t0) REVERT: I 433 ARG cc_start: 0.7191 (OUTLIER) cc_final: 0.6829 (tpt170) REVERT: I 486 TYR cc_start: 0.8175 (t80) cc_final: 0.7844 (t80) REVERT: K 109 MET cc_start: 0.7652 (mmm) cc_final: 0.7324 (mmm) REVERT: L 74 LYS cc_start: 0.7514 (mtmm) cc_final: 0.6929 (mtmt) outliers start: 58 outliers final: 38 residues processed: 344 average time/residue: 0.3149 time to fit residues: 167.8390 Evaluate side-chains 327 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 285 time to evaluate : 2.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 433 ARG Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 74 LYS Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain E residue 278 LYS Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 433 ARG Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 32 ASN Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain I residue 148 MET Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 262 SER Chi-restraints excluded: chain I residue 271 THR Chi-restraints excluded: chain I residue 278 LYS Chi-restraints excluded: chain I residue 299 THR Chi-restraints excluded: chain I residue 433 ARG Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 75 ASP Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain L residue 79 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 79 optimal weight: 10.0000 chunk 211 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 137 optimal weight: 0.6980 chunk 57 optimal weight: 9.9990 chunk 235 optimal weight: 7.9990 chunk 195 optimal weight: 4.9990 chunk 108 optimal weight: 0.1980 chunk 19 optimal weight: 2.9990 chunk 77 optimal weight: 20.0000 chunk 123 optimal weight: 6.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 377 ASN E 408 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 469 HIS ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 20550 Z= 0.289 Angle : 0.662 9.867 27795 Z= 0.334 Chirality : 0.046 0.403 3048 Planarity : 0.005 0.065 3567 Dihedral : 8.132 50.456 3271 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 3.60 % Allowed : 18.49 % Favored : 77.92 % 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: -1.29 (0.17), residues: 2472 helix: 1.11 (0.21), residues: 600 sheet: -1.25 (0.22), residues: 549 loop : -1.65 (0.16), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 150 HIS 0.014 0.001 HIS E 353 PHE 0.015 0.002 PHE I 372 TYR 0.018 0.002 TYR C 82 ARG 0.007 0.001 ARG G 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 309 time to evaluate : 2.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.7364 (tp30) cc_final: 0.7088 (tp30) REVERT: A 83 GLU cc_start: 0.7666 (tt0) cc_final: 0.7389 (tt0) REVERT: A 337 ILE cc_start: 0.8985 (mm) cc_final: 0.8603 (mm) REVERT: A 411 MET cc_start: 0.8930 (tmm) cc_final: 0.8136 (tmm) REVERT: A 425 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8717 (tp) REVERT: A 433 ARG cc_start: 0.7619 (OUTLIER) cc_final: 0.7037 (mmp80) REVERT: C 31 ASP cc_start: 0.7798 (p0) cc_final: 0.7511 (p0) REVERT: C 144 LEU cc_start: 0.5110 (tt) cc_final: 0.4850 (mp) REVERT: D 69 THR cc_start: 0.6812 (p) cc_final: 0.6532 (p) REVERT: E 56 ASP cc_start: 0.6054 (t0) cc_final: 0.5796 (t0) REVERT: E 115 LYS cc_start: 0.7448 (ttmt) cc_final: 0.6925 (ttmt) REVERT: E 146 ARG cc_start: 0.7157 (mmt-90) cc_final: 0.6887 (mmt-90) REVERT: E 308 LYS cc_start: 0.8625 (mtpp) cc_final: 0.8304 (mttt) REVERT: E 425 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8782 (tp) REVERT: E 433 ARG cc_start: 0.6924 (OUTLIER) cc_final: 0.5635 (mtt-85) REVERT: G 12 VAL cc_start: 0.8304 (t) cc_final: 0.8031 (m) REVERT: I 83 GLU cc_start: 0.7362 (tt0) cc_final: 0.7058 (tt0) REVERT: I 298 LEU cc_start: 0.8769 (mt) cc_final: 0.8484 (mp) REVERT: I 308 LYS cc_start: 0.8581 (mtpp) cc_final: 0.8345 (mttp) REVERT: I 324 ILE cc_start: 0.7763 (mt) cc_final: 0.7390 (pt) REVERT: I 355 ASN cc_start: 0.8559 (t0) cc_final: 0.8169 (t0) REVERT: I 433 ARG cc_start: 0.7071 (OUTLIER) cc_final: 0.6857 (tpt170) REVERT: I 486 TYR cc_start: 0.8178 (t80) cc_final: 0.7853 (t80) REVERT: K 109 MET cc_start: 0.7925 (mmm) cc_final: 0.7614 (mmm) REVERT: L 74 LYS cc_start: 0.7446 (mtmm) cc_final: 0.6893 (mtmt) outliers start: 78 outliers final: 56 residues processed: 358 average time/residue: 0.3048 time to fit residues: 168.6414 Evaluate side-chains 350 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 289 time to evaluate : 2.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 433 ARG Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 98 CYS Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 278 LYS Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 425 LEU Chi-restraints excluded: chain E residue 433 ARG Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 32 ASN Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain I residue 148 MET Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 262 SER Chi-restraints excluded: chain I residue 271 THR Chi-restraints excluded: chain I residue 278 LYS Chi-restraints excluded: chain I residue 299 THR Chi-restraints excluded: chain I residue 382 VAL Chi-restraints excluded: chain I residue 393 VAL Chi-restraints excluded: chain I residue 433 ARG Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 75 ASP Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 94 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 226 optimal weight: 20.0000 chunk 26 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 171 optimal weight: 2.9990 chunk 197 optimal weight: 9.9990 chunk 131 optimal weight: 20.0000 chunk 234 optimal weight: 20.0000 chunk 146 optimal weight: 30.0000 chunk 142 optimal weight: 10.0000 chunk 108 optimal weight: 10.0000 chunk 144 optimal weight: 10.0000 overall best weight: 5.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 377 ASN ** E 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 53 ASN H 79 GLN ** I 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 477 ASN L 53 ASN ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.081 20550 Z= 0.519 Angle : 0.796 14.706 27795 Z= 0.404 Chirality : 0.051 0.439 3048 Planarity : 0.005 0.062 3567 Dihedral : 8.436 47.543 3267 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 3.96 % Allowed : 19.23 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.04 % 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: -1.69 (0.16), residues: 2472 helix: 0.77 (0.21), residues: 600 sheet: -1.44 (0.22), residues: 582 loop : -1.92 (0.16), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP A 150 HIS 0.013 0.002 HIS E 353 PHE 0.020 0.003 PHE I 415 TYR 0.023 0.002 TYR E 9 ARG 0.011 0.001 ARG G 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 301 time to evaluate : 2.080 Fit side-chains revert: symmetry clash REVERT: A 36 GLU cc_start: 0.7397 (tp30) cc_final: 0.7110 (tp30) REVERT: A 337 ILE cc_start: 0.8997 (mm) cc_final: 0.8588 (mm) REVERT: A 349 TYR cc_start: 0.9136 (OUTLIER) cc_final: 0.8366 (m-80) REVERT: A 425 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8643 (tp) REVERT: A 433 ARG cc_start: 0.7646 (OUTLIER) cc_final: 0.6899 (mtt-85) REVERT: C 144 LEU cc_start: 0.5138 (tt) cc_final: 0.4838 (mp) REVERT: D 69 THR cc_start: 0.7016 (p) cc_final: 0.6704 (p) REVERT: E 36 GLU cc_start: 0.7340 (tp30) cc_final: 0.6966 (tp30) REVERT: E 63 LEU cc_start: 0.9241 (mt) cc_final: 0.9027 (mt) REVERT: E 146 ARG cc_start: 0.7641 (mmt-90) cc_final: 0.7373 (mmt-90) REVERT: E 265 ILE cc_start: 0.9176 (OUTLIER) cc_final: 0.8906 (mt) REVERT: E 308 LYS cc_start: 0.8668 (mtpp) cc_final: 0.8317 (mttm) REVERT: E 433 ARG cc_start: 0.7244 (OUTLIER) cc_final: 0.6412 (tpt-90) REVERT: G 12 VAL cc_start: 0.8345 (t) cc_final: 0.8058 (m) REVERT: I 33 ASP cc_start: 0.8237 (t0) cc_final: 0.7616 (t0) REVERT: I 274 ASN cc_start: 0.6464 (p0) cc_final: 0.5913 (p0) REVERT: I 432 GLU cc_start: 0.7662 (tp30) cc_final: 0.7123 (tp30) REVERT: I 433 ARG cc_start: 0.7401 (OUTLIER) cc_final: 0.6922 (tpt170) REVERT: I 486 TYR cc_start: 0.8200 (t80) cc_final: 0.7932 (t80) REVERT: K 19 ARG cc_start: 0.7187 (tpp-160) cc_final: 0.6939 (ttm-80) REVERT: K 85 MET cc_start: 0.6842 (OUTLIER) cc_final: 0.6583 (mtt) REVERT: K 109 MET cc_start: 0.8048 (mmm) cc_final: 0.7793 (mmm) REVERT: L 74 LYS cc_start: 0.7137 (mtmm) cc_final: 0.6434 (mtmt) REVERT: L 91 PHE cc_start: 0.8419 (OUTLIER) cc_final: 0.8087 (m-10) outliers start: 86 outliers final: 66 residues processed: 361 average time/residue: 0.2925 time to fit residues: 163.9821 Evaluate side-chains 356 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 282 time to evaluate : 2.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 349 TYR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 433 ARG Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 98 CYS Chi-restraints excluded: chain C residue 147 MET Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 278 LYS Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 349 TYR Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 433 ARG Chi-restraints excluded: chain E residue 475 CYS Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 32 ASN Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 148 MET Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 239 THR Chi-restraints excluded: chain I residue 252 GLU Chi-restraints excluded: chain I residue 262 SER Chi-restraints excluded: chain I residue 271 THR Chi-restraints excluded: chain I residue 278 LYS Chi-restraints excluded: chain I residue 299 THR Chi-restraints excluded: chain I residue 382 VAL Chi-restraints excluded: chain I residue 393 VAL Chi-restraints excluded: chain I residue 433 ARG Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 75 ASP Chi-restraints excluded: chain K residue 85 MET Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain L residue 91 PHE Chi-restraints excluded: chain L residue 94 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 93 optimal weight: 0.9990 chunk 139 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 148 optimal weight: 5.9990 chunk 159 optimal weight: 6.9990 chunk 115 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 chunk 184 optimal weight: 3.9990 chunk 213 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 377 ASN ** E 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 477 ASN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 79 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 20550 Z= 0.211 Angle : 0.644 11.258 27795 Z= 0.325 Chirality : 0.045 0.404 3048 Planarity : 0.004 0.064 3567 Dihedral : 7.457 42.346 3267 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.04 % Allowed : 20.47 % Favored : 76.49 % 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: -1.40 (0.17), residues: 2472 helix: 1.17 (0.21), residues: 600 sheet: -1.38 (0.21), residues: 570 loop : -1.75 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP I 150 HIS 0.015 0.001 HIS E 353 PHE 0.022 0.002 PHE K 70 TYR 0.016 0.002 TYR C 82 ARG 0.009 0.001 ARG G 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 319 time to evaluate : 2.253 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 GLU cc_start: 0.7761 (tt0) cc_final: 0.7509 (tt0) REVERT: A 337 ILE cc_start: 0.8977 (mm) cc_final: 0.8593 (mm) REVERT: A 349 TYR cc_start: 0.9078 (OUTLIER) cc_final: 0.8279 (m-80) REVERT: A 411 MET cc_start: 0.8730 (tmm) cc_final: 0.8308 (tmm) REVERT: A 433 ARG cc_start: 0.7131 (OUTLIER) cc_final: 0.6300 (mmt180) REVERT: C 31 ASP cc_start: 0.8126 (p0) cc_final: 0.7663 (p0) REVERT: C 34 MET cc_start: 0.8201 (tpp) cc_final: 0.7388 (tpp) REVERT: C 144 LEU cc_start: 0.5129 (tt) cc_final: 0.4858 (mp) REVERT: D 69 THR cc_start: 0.6817 (p) cc_final: 0.6551 (p) REVERT: E 308 LYS cc_start: 0.8677 (mtpp) cc_final: 0.8330 (mttt) REVERT: E 476 MET cc_start: 0.7483 (mtm) cc_final: 0.7169 (mtm) REVERT: G 12 VAL cc_start: 0.8278 (t) cc_final: 0.8025 (m) REVERT: H 4 MET cc_start: 0.8338 (mtp) cc_final: 0.7980 (mtm) REVERT: I 433 ARG cc_start: 0.7339 (OUTLIER) cc_final: 0.6381 (mmp-170) REVERT: K 109 MET cc_start: 0.8103 (mmm) cc_final: 0.7765 (mmm) REVERT: L 74 LYS cc_start: 0.6853 (mtmm) cc_final: 0.6127 (mtmt) outliers start: 66 outliers final: 52 residues processed: 358 average time/residue: 0.3091 time to fit residues: 170.1704 Evaluate side-chains 338 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 283 time to evaluate : 2.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 349 TYR Chi-restraints excluded: chain A residue 353 HIS Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 433 ARG Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 278 LYS Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 349 TYR Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 475 CYS Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 32 ASN Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain I residue 148 MET Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 239 THR Chi-restraints excluded: chain I residue 278 LYS Chi-restraints excluded: chain I residue 299 THR Chi-restraints excluded: chain I residue 382 VAL Chi-restraints excluded: chain I residue 393 VAL Chi-restraints excluded: chain I residue 433 ARG Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 75 ASP Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 94 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 224 optimal weight: 30.0000 chunk 204 optimal weight: 0.9990 chunk 218 optimal weight: 20.0000 chunk 131 optimal weight: 8.9990 chunk 95 optimal weight: 10.0000 chunk 171 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 197 optimal weight: 7.9990 chunk 206 optimal weight: 4.9990 chunk 217 optimal weight: 2.9990 chunk 143 optimal weight: 20.0000 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 HIS C 78 GLN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 377 ASN ** E 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 79 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 20550 Z= 0.275 Angle : 0.666 12.552 27795 Z= 0.336 Chirality : 0.046 0.408 3048 Planarity : 0.005 0.062 3567 Dihedral : 7.193 40.236 3263 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 3.23 % Allowed : 20.47 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.32 (0.17), residues: 2472 helix: 1.23 (0.21), residues: 600 sheet: -1.34 (0.22), residues: 540 loop : -1.71 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 150 HIS 0.016 0.001 HIS E 353 PHE 0.018 0.002 PHE G 70 TYR 0.023 0.002 TYR E 192 ARG 0.008 0.001 ARG E 433 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 292 time to evaluate : 2.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.7269 (tp30) cc_final: 0.6927 (tp30) REVERT: A 83 GLU cc_start: 0.7693 (tt0) cc_final: 0.7472 (tt0) REVERT: A 337 ILE cc_start: 0.8999 (mm) cc_final: 0.8586 (mm) REVERT: A 349 TYR cc_start: 0.9053 (OUTLIER) cc_final: 0.8264 (m-80) REVERT: A 425 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8724 (tp) REVERT: A 433 ARG cc_start: 0.7249 (OUTLIER) cc_final: 0.7017 (mpt180) REVERT: C 144 LEU cc_start: 0.5092 (tt) cc_final: 0.4847 (mp) REVERT: D 69 THR cc_start: 0.6841 (p) cc_final: 0.6550 (p) REVERT: E 308 LYS cc_start: 0.8695 (mtpp) cc_final: 0.8345 (mttt) REVERT: G 12 VAL cc_start: 0.8282 (t) cc_final: 0.7962 (m) REVERT: G 75 ASP cc_start: 0.6329 (OUTLIER) cc_final: 0.5503 (t0) REVERT: H 4 MET cc_start: 0.8335 (mtp) cc_final: 0.7996 (mtm) REVERT: I 433 ARG cc_start: 0.7320 (OUTLIER) cc_final: 0.6435 (mmp-170) REVERT: K 109 MET cc_start: 0.8090 (mmm) cc_final: 0.7744 (mmm) REVERT: L 74 LYS cc_start: 0.6850 (mtmm) cc_final: 0.6098 (mtmt) REVERT: L 92 TRP cc_start: 0.7339 (t-100) cc_final: 0.7127 (t60) outliers start: 70 outliers final: 57 residues processed: 343 average time/residue: 0.3312 time to fit residues: 177.3018 Evaluate side-chains 344 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 282 time to evaluate : 2.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 349 TYR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 433 ARG Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 98 CYS Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 349 TYR Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 475 CYS Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 75 ASP Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 32 ASN Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain I residue 148 MET Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 239 THR Chi-restraints excluded: chain I residue 262 SER Chi-restraints excluded: chain I residue 278 LYS Chi-restraints excluded: chain I residue 299 THR Chi-restraints excluded: chain I residue 308 LYS Chi-restraints excluded: chain I residue 351 TYR Chi-restraints excluded: chain I residue 382 VAL Chi-restraints excluded: chain I residue 393 VAL Chi-restraints excluded: chain I residue 433 ARG Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 75 ASP Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain L residue 32 ASN Chi-restraints excluded: chain L residue 79 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 230 optimal weight: 20.0000 chunk 140 optimal weight: 0.8980 chunk 109 optimal weight: 4.9990 chunk 160 optimal weight: 0.9990 chunk 242 optimal weight: 8.9990 chunk 222 optimal weight: 0.8980 chunk 192 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 148 optimal weight: 30.0000 chunk 118 optimal weight: 0.9990 chunk 153 optimal weight: 20.0000 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 241 ASN E 377 ASN E 469 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 194 ASN L 38 GLN ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 20550 Z= 0.183 Angle : 0.633 12.579 27795 Z= 0.318 Chirality : 0.045 0.393 3048 Planarity : 0.004 0.062 3567 Dihedral : 6.609 45.139 3263 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.54 % Allowed : 21.21 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.17), residues: 2472 helix: 1.40 (0.21), residues: 603 sheet: -1.30 (0.22), residues: 540 loop : -1.62 (0.17), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP I 150 HIS 0.017 0.001 HIS E 353 PHE 0.015 0.001 PHE K 70 TYR 0.029 0.001 TYR C 82 ARG 0.008 0.001 ARG A 88 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 309 time to evaluate : 2.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 GLU cc_start: 0.7869 (tt0) cc_final: 0.7636 (tt0) REVERT: A 337 ILE cc_start: 0.8987 (mm) cc_final: 0.8590 (mm) REVERT: A 349 TYR cc_start: 0.9043 (OUTLIER) cc_final: 0.8261 (m-80) REVERT: A 411 MET cc_start: 0.8863 (tmm) cc_final: 0.8415 (tmm) REVERT: A 429 MET cc_start: 0.6794 (mtp) cc_final: 0.6217 (mtt) REVERT: A 433 ARG cc_start: 0.7289 (OUTLIER) cc_final: 0.6426 (mmt180) REVERT: C 109 MET cc_start: 0.7830 (mmm) cc_final: 0.7560 (mmm) REVERT: E 162 LYS cc_start: 0.6987 (tppp) cc_final: 0.6512 (tptp) REVERT: E 308 LYS cc_start: 0.8680 (mtpp) cc_final: 0.8336 (mttt) REVERT: G 12 VAL cc_start: 0.8281 (t) cc_final: 0.7847 (m) REVERT: H 4 MET cc_start: 0.8151 (mtp) cc_final: 0.7770 (mtm) REVERT: I 148 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.8315 (mmp) REVERT: I 355 ASN cc_start: 0.8496 (t0) cc_final: 0.8204 (t0) REVERT: I 433 ARG cc_start: 0.7150 (OUTLIER) cc_final: 0.6296 (mmp-170) REVERT: K 109 MET cc_start: 0.8052 (mmm) cc_final: 0.7818 (mmm) REVERT: K 144 LEU cc_start: 0.4989 (mp) cc_final: 0.4768 (tt) REVERT: L 74 LYS cc_start: 0.6848 (mtmm) cc_final: 0.6139 (mtmt) REVERT: L 134 MET cc_start: 0.2805 (mtp) cc_final: 0.2101 (mtp) outliers start: 55 outliers final: 45 residues processed: 346 average time/residue: 0.3035 time to fit residues: 162.8039 Evaluate side-chains 339 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 290 time to evaluate : 2.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 349 TYR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 433 ARG Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 349 TYR Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 475 CYS Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 32 ASN Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 148 MET Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 194 ASN Chi-restraints excluded: chain I residue 239 THR Chi-restraints excluded: chain I residue 299 THR Chi-restraints excluded: chain I residue 308 LYS Chi-restraints excluded: chain I residue 351 TYR Chi-restraints excluded: chain I residue 382 VAL Chi-restraints excluded: chain I residue 393 VAL Chi-restraints excluded: chain I residue 433 ARG Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 118 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 177 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 53 optimal weight: 0.0970 chunk 193 optimal weight: 3.9990 chunk 80 optimal weight: 7.9990 chunk 198 optimal weight: 8.9990 chunk 24 optimal weight: 8.9990 chunk 35 optimal weight: 10.0000 chunk 169 optimal weight: 9.9990 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 353 HIS E 377 ASN ** E 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 194 ASN ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.181475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.171148 restraints weight = 25687.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.168946 restraints weight = 45941.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.168104 restraints weight = 64169.045| |-----------------------------------------------------------------------------| r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.162 20550 Z= 0.278 Angle : 0.798 59.156 27795 Z= 0.438 Chirality : 0.049 0.929 3048 Planarity : 0.005 0.063 3567 Dihedral : 6.617 45.261 3263 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.67 % Allowed : 21.07 % Favored : 76.26 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.17), residues: 2472 helix: 1.40 (0.21), residues: 603 sheet: -1.28 (0.22), residues: 540 loop : -1.62 (0.17), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP I 150 HIS 0.009 0.001 HIS E 353 PHE 0.014 0.001 PHE I 372 TYR 0.025 0.001 TYR C 82 ARG 0.011 0.001 ARG D 126 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3902.94 seconds wall clock time: 72 minutes 42.48 seconds (4362.48 seconds total)