Starting phenix.real_space_refine on Tue Dec 12 04:06:13 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dkj_30707/12_2023/7dkj_30707.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dkj_30707/12_2023/7dkj_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_30707/12_2023/7dkj_30707.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dkj_30707/12_2023/7dkj_30707.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dkj_30707/12_2023/7dkj_30707.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dkj_30707/12_2023/7dkj_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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 6 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: 6 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: 6 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: 6 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: 6 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: 6 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: 10.53, 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: 8.43 Conformation dependent library (CDL) restraints added in 3.4 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: 2.03 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: 6.49 Time building geometry restraints manager: 8.98 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: 11292 21.28 - 42.56: 949 42.56 - 63.84: 163 63.84 - 85.11: 83 85.11 - 106.39: 80 Dihedral angle restraints: 12567 sinusoidal: 5415 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 12564 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: 0.240 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: 1.910 Check model and map are aligned: 0.300 Set scattering table: 0.170 Process input model: 52.550 Find NCS groups from input model: 1.120 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.040 ------------------------------------------------------------------------------- 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 : 18.799 106.392 7926 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 : 2.466 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 outliers start: 40 outliers final: 7 residues processed: 444 average time/residue: 0.3273 time to fit residues: 220.3500 Evaluate side-chains 324 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 317 time to evaluate : 2.431 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.3931 time to fit residues: 6.9875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 102 optimal weight: 7.9990 chunk 62 optimal weight: 30.0000 chunk 124 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 190 optimal weight: 0.7980 chunk 73 optimal weight: 7.9990 chunk 115 optimal weight: 0.6980 chunk 141 optimal weight: 8.9990 chunk 220 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 A 477 ASN 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: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20550 Z= 0.207 Angle : 0.690 8.529 27795 Z= 0.353 Chirality : 0.048 0.398 3048 Planarity : 0.005 0.055 3567 Dihedral : 13.246 83.394 3141 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.98 % Allowed : 11.53 % Favored : 86.49 % 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: -1.53 (0.16), residues: 2472 helix: 0.73 (0.22), residues: 594 sheet: -1.25 (0.21), residues: 564 loop : -1.75 (0.16), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 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 62 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 381 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 338 time to evaluate : 2.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 24 residues processed: 362 average time/residue: 0.3180 time to fit residues: 178.9426 Evaluate side-chains 312 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 288 time to evaluate : 2.169 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1890 time to fit residues: 11.2160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 122 optimal weight: 5.9990 chunk 68 optimal weight: 9.9990 chunk 183 optimal weight: 2.9990 chunk 150 optimal weight: 8.9990 chunk 60 optimal weight: 10.0000 chunk 221 optimal weight: 1.9990 chunk 238 optimal weight: 20.0000 chunk 196 optimal weight: 4.9990 chunk 219 optimal weight: 9.9990 chunk 75 optimal weight: 0.0770 chunk 177 optimal weight: 3.9990 overall best weight: 2.8146 ------------------------------------------------------------------------------- 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 406 ASN C 157 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 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 241 ASN E 377 ASN E 477 ASN G 157 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 146 GLN ** I 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 477 ASN K 157 GLN L 79 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 20550 Z= 0.305 Angle : 0.697 8.579 27795 Z= 0.353 Chirality : 0.048 0.402 3048 Planarity : 0.005 0.058 3567 Dihedral : 10.455 68.824 3141 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 2.07 % Allowed : 14.85 % Favored : 83.08 % 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: -1.38 (0.17), residues: 2472 helix: 1.12 (0.21), residues: 594 sheet: -1.33 (0.22), residues: 549 loop : -1.72 (0.16), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP I 150 HIS 0.005 0.001 HIS H 90 PHE 0.014 0.002 PHE I 372 TYR 0.032 0.002 TYR K 82 ARG 0.007 0.001 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 368 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 323 time to evaluate : 2.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 24 residues processed: 355 average time/residue: 0.3165 time to fit residues: 174.4521 Evaluate side-chains 304 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 280 time to evaluate : 2.071 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.2381 time to fit residues: 13.0261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 218 optimal weight: 8.9990 chunk 166 optimal weight: 0.9990 chunk 114 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 chunk 148 optimal weight: 0.9990 chunk 221 optimal weight: 5.9990 chunk 234 optimal weight: 20.0000 chunk 115 optimal weight: 4.9990 chunk 210 optimal weight: 0.9980 chunk 63 optimal weight: 8.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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** ** D 79 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 377 ASN E 469 HIS E 477 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 20550 Z= 0.288 Angle : 0.673 11.562 27795 Z= 0.339 Chirality : 0.047 0.403 3048 Planarity : 0.005 0.061 3567 Dihedral : 8.955 57.803 3141 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 1.75 % Allowed : 18.35 % Favored : 79.90 % 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: -1.39 (0.17), residues: 2472 helix: 1.09 (0.21), residues: 603 sheet: -1.41 (0.21), residues: 582 loop : -1.69 (0.16), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 150 HIS 0.005 0.001 HIS E 353 PHE 0.013 0.002 PHE I 372 TYR 0.017 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 346 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 308 time to evaluate : 2.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 26 residues processed: 331 average time/residue: 0.3042 time to fit residues: 157.9507 Evaluate side-chains 310 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 284 time to evaluate : 2.222 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.1931 time to fit residues: 12.3031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 195 optimal weight: 7.9990 chunk 133 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 174 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 200 optimal weight: 4.9990 chunk 162 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 119 optimal weight: 5.9990 chunk 210 optimal weight: 3.9990 chunk 59 optimal weight: 0.0980 overall best weight: 3.6188 ------------------------------------------------------------------------------- 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** D 53 ASN ** D 79 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 377 ASN E 408 ASN 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** K 78 GLN L 53 ASN ** 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: 0.7310 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 20550 Z= 0.345 Angle : 0.697 10.602 27795 Z= 0.352 Chirality : 0.047 0.413 3048 Planarity : 0.005 0.060 3567 Dihedral : 8.394 54.194 3141 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 1.80 % Allowed : 19.55 % 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: -1.41 (0.17), residues: 2472 helix: 1.03 (0.21), residues: 600 sheet: -1.36 (0.22), residues: 552 loop : -1.71 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 150 HIS 0.010 0.001 HIS E 469 PHE 0.015 0.002 PHE I 372 TYR 0.023 0.002 TYR G 82 ARG 0.006 0.001 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 348 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 309 time to evaluate : 2.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 28 residues processed: 337 average time/residue: 0.3154 time to fit residues: 166.1065 Evaluate side-chains 308 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 280 time to evaluate : 2.353 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.1857 time to fit residues: 12.9831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 79 optimal weight: 3.9990 chunk 211 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 137 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 235 optimal weight: 20.0000 chunk 195 optimal weight: 5.9990 chunk 108 optimal weight: 6.9990 chunk 19 optimal weight: 7.9990 chunk 77 optimal weight: 20.0000 chunk 123 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 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 377 ASN E 477 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 78 GLN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 79 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 20550 Z= 0.299 Angle : 0.671 11.844 27795 Z= 0.338 Chirality : 0.046 0.411 3048 Planarity : 0.005 0.064 3567 Dihedral : 7.818 49.862 3141 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 1.52 % Allowed : 20.47 % Favored : 78.01 % 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: 1.00 (0.21), residues: 606 sheet: -1.35 (0.22), residues: 540 loop : -1.70 (0.16), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 150 HIS 0.013 0.001 HIS E 469 PHE 0.015 0.002 PHE I 372 TYR 0.023 0.002 TYR C 82 ARG 0.006 0.001 ARG A 88 *********************** 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 334 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 301 time to evaluate : 2.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 18 residues processed: 319 average time/residue: 0.3229 time to fit residues: 160.5153 Evaluate side-chains 293 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 275 time to evaluate : 2.210 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1922 time to fit residues: 9.5334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 133 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 chunk 197 optimal weight: 9.9990 chunk 131 optimal weight: 10.0000 chunk 234 optimal weight: 20.0000 chunk 146 optimal weight: 30.0000 chunk 142 optimal weight: 2.9990 chunk 108 optimal weight: 7.9990 chunk 144 optimal weight: 6.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- 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** ** D 79 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 377 ASN ** 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 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 20550 Z= 0.314 Angle : 0.678 12.092 27795 Z= 0.342 Chirality : 0.047 0.413 3048 Planarity : 0.005 0.062 3567 Dihedral : 7.497 47.144 3141 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 1.43 % Allowed : 20.89 % Favored : 77.69 % 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: -1.39 (0.17), residues: 2472 helix: 1.12 (0.21), residues: 600 sheet: -1.34 (0.22), residues: 540 loop : -1.74 (0.16), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 150 HIS 0.010 0.001 HIS E 469 PHE 0.022 0.002 PHE K 70 TYR 0.023 0.002 TYR G 82 ARG 0.011 0.001 ARG D 126 *********************** 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 323 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 292 time to evaluate : 2.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 14 residues processed: 313 average time/residue: 0.3181 time to fit residues: 157.0337 Evaluate side-chains 287 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 273 time to evaluate : 2.424 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1956 time to fit residues: 8.4037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 93 optimal weight: 10.0000 chunk 139 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 148 optimal weight: 30.0000 chunk 159 optimal weight: 6.9990 chunk 115 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 184 optimal weight: 8.9990 chunk 213 optimal weight: 10.0000 overall best weight: 4.7788 ------------------------------------------------------------------------------- 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** D 79 GLN ** 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** ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 20550 Z= 0.432 Angle : 0.754 14.000 27795 Z= 0.383 Chirality : 0.049 0.429 3048 Planarity : 0.005 0.062 3567 Dihedral : 7.582 44.607 3141 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 1.48 % Allowed : 20.98 % Favored : 77.55 % 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: -1.63 (0.16), residues: 2472 helix: 0.80 (0.21), residues: 606 sheet: -1.42 (0.21), residues: 570 loop : -1.87 (0.16), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A 150 HIS 0.013 0.002 HIS E 469 PHE 0.018 0.002 PHE I 372 TYR 0.028 0.002 TYR C 82 ARG 0.008 0.001 ARG D 126 *********************** 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 316 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 284 time to evaluate : 2.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 18 residues processed: 302 average time/residue: 0.3140 time to fit residues: 148.7306 Evaluate side-chains 279 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 261 time to evaluate : 2.329 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2095 time to fit residues: 10.1432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 218 optimal weight: 3.9990 chunk 131 optimal weight: 9.9990 chunk 95 optimal weight: 0.8980 chunk 171 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 197 optimal weight: 1.9990 chunk 206 optimal weight: 0.6980 chunk 217 optimal weight: 0.9990 chunk 143 optimal weight: 20.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN C 78 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 377 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 147 ASN I 194 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20550 Z= 0.197 Angle : 0.649 11.594 27795 Z= 0.328 Chirality : 0.045 0.400 3048 Planarity : 0.004 0.063 3567 Dihedral : 6.819 41.451 3141 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.46 % Allowed : 21.95 % Favored : 77.59 % 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: 1.21 (0.21), residues: 603 sheet: -1.33 (0.22), residues: 540 loop : -1.70 (0.16), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP I 150 HIS 0.016 0.001 HIS E 469 PHE 0.015 0.002 PHE K 70 TYR 0.029 0.002 TYR C 82 ARG 0.008 0.001 ARG A 88 *********************** 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 320 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 310 time to evaluate : 2.211 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 315 average time/residue: 0.3215 time to fit residues: 156.4549 Evaluate side-chains 282 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 276 time to evaluate : 2.262 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1792 time to fit residues: 5.1523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 230 optimal weight: 30.0000 chunk 140 optimal weight: 0.9980 chunk 109 optimal weight: 4.9990 chunk 160 optimal weight: 0.0050 chunk 242 optimal weight: 6.9990 chunk 222 optimal weight: 1.9990 chunk 192 optimal weight: 0.0070 chunk 20 optimal weight: 2.9990 chunk 148 optimal weight: 30.0000 chunk 118 optimal weight: 6.9990 chunk 153 optimal weight: 20.0000 overall best weight: 1.2016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN A 353 HIS C 78 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 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 353 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 20550 Z= 0.202 Angle : 0.647 11.315 27795 Z= 0.325 Chirality : 0.045 0.393 3048 Planarity : 0.004 0.063 3567 Dihedral : 6.393 46.281 3141 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.32 % Allowed : 23.42 % Favored : 76.26 % 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: -1.20 (0.17), residues: 2472 helix: 1.32 (0.21), residues: 603 sheet: -1.25 (0.22), residues: 540 loop : -1.64 (0.17), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP I 150 HIS 0.008 0.001 HIS E 469 PHE 0.017 0.001 PHE I 372 TYR 0.029 0.002 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 297 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 290 time to evaluate : 2.109 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 293 average time/residue: 0.3167 time to fit residues: 144.7221 Evaluate side-chains 282 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 279 time to evaluate : 2.224 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2223 time to fit residues: 4.2978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 10.0000 chunk 59 optimal weight: 0.6980 chunk 177 optimal weight: 0.0060 chunk 28 optimal weight: 8.9990 chunk 53 optimal weight: 10.0000 chunk 193 optimal weight: 4.9990 chunk 80 optimal weight: 20.0000 chunk 198 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 169 optimal weight: 0.9980 overall best weight: 1.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.180691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.170825 restraints weight = 26067.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.170479 restraints weight = 42160.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.169161 restraints weight = 42690.415| |-----------------------------------------------------------------------------| r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 20550 Z= 0.204 Angle : 0.632 11.048 27795 Z= 0.320 Chirality : 0.045 0.388 3048 Planarity : 0.004 0.065 3567 Dihedral : 6.135 50.467 3141 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.14 % Allowed : 23.42 % Favored : 76.44 % 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: -1.16 (0.17), residues: 2472 helix: 1.37 (0.21), residues: 603 sheet: -1.23 (0.22), residues: 540 loop : -1.63 (0.17), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP I 150 HIS 0.007 0.001 HIS E 469 PHE 0.016 0.001 PHE I 372 TYR 0.029 0.002 TYR C 82 ARG 0.009 0.001 ARG K 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3797.73 seconds wall clock time: 70 minutes 57.20 seconds (4257.20 seconds total)