Starting phenix.real_space_refine on Fri Mar 15 21:52:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swd_25471/03_2024/7swd_25471.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swd_25471/03_2024/7swd_25471.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swd_25471/03_2024/7swd_25471.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swd_25471/03_2024/7swd_25471.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swd_25471/03_2024/7swd_25471.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swd_25471/03_2024/7swd_25471.pdb" } resolution = 3.59 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= 0.005 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 56 5.16 5 C 8124 2.51 5 N 2205 2.21 5 O 2448 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 100": "OE1" <-> "OE2" Residue "A PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 552": "OD1" <-> "OD2" Residue "C GLU 106": "OE1" <-> "OE2" Residue "C ASP 117": "OD1" <-> "OD2" Residue "E TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 156": "OE1" <-> "OE2" Residue "E PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 545": "OE1" <-> "OE2" Residue "G GLU 227": "OE1" <-> "OE2" Residue "H ASP 74": "OD1" <-> "OD2" Residue "H TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 90": "OE1" <-> "OE2" Residue "H TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 109": "OD1" <-> "OD2" Residue "I GLU 10": "OE1" <-> "OE2" Residue "I ASP 142": "OD1" <-> "OD2" Residue "J TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 88": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12833 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1153 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 10, 'TRANS': 140} Chain breaks: 1 Chain: "B" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 758 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "C" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1153 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 10, 'TRANS': 140} Chain breaks: 1 Chain: "D" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 758 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "E" Number of atoms: 1120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1120 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 10, 'TRANS': 136} Chain breaks: 2 Chain: "F" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 758 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "G" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1734 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 213} Chain breaks: 1 Chain: "H" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1734 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 213} Chain breaks: 1 Chain: "I" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1760 Classifications: {'peptide': 229} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 216} Chain breaks: 1 Chain: "J" Number of atoms: 916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 916 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "K" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 872 Classifications: {'peptide': 113} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 106} 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: "L" 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 Time building chain proxies: 7.41, per 1000 atoms: 0.58 Number of scatterers: 12833 At special positions: 0 Unit cell: (133.1, 126.5, 104.5, 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 56 16.00 O 2448 8.00 N 2205 7.00 C 8124 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 135 " distance=2.03 Simple disulfide: pdb=" SG CYS A 121 " - pdb=" SG CYS A 147 " distance=2.04 Simple disulfide: pdb=" SG CYS B 511 " - pdb=" SG CYS B 556 " distance=2.03 Simple disulfide: pdb=" SG CYS C 108 " - pdb=" SG CYS C 135 " distance=2.03 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 147 " distance=2.03 Simple disulfide: pdb=" SG CYS D 511 " - pdb=" SG CYS D 556 " distance=2.04 Simple disulfide: pdb=" SG CYS E 108 " - pdb=" SG CYS E 135 " distance=2.03 Simple disulfide: pdb=" SG CYS E 121 " - pdb=" SG CYS E 147 " distance=2.03 Simple disulfide: pdb=" SG CYS F 511 " - pdb=" SG CYS F 556 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 97 " distance=2.03 Simple disulfide: pdb=" SG CYS G 164 " - pdb=" SG CYS G 234 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS H 164 " - pdb=" SG CYS H 234 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 97 " distance=2.03 Simple disulfide: pdb=" SG CYS I 164 " - pdb=" SG CYS I 234 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 94 " 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 L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 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-ASN " NAG L 1 " - " ASN B 563 " " NAG M 1 " - " ASN D 563 " " NAG N 1 " - " ASN F 563 " Time building additional restraints: 5.39 Conformation dependent library (CDL) restraints added in 2.3 seconds 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2954 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 33 sheets defined 12.0% alpha, 30.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'A' and resid 59 through 61 No H-bonds generated for 'chain 'A' and resid 59 through 61' Processing helix chain 'A' and resid 71 through 73 No H-bonds generated for 'chain 'A' and resid 71 through 73' Processing helix chain 'A' and resid 78 through 84 removed outlier: 3.733A pdb=" N LYS A 84 " --> pdb=" O PRO A 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 527 removed outlier: 4.275A pdb=" N ALA B 525 " --> pdb=" O ASP B 522 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ILE B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 536 Processing helix chain 'B' and resid 551 through 576 removed outlier: 4.956A pdb=" N GLN B 567 " --> pdb=" O ASN B 563 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ALA B 568 " --> pdb=" O GLU B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 598 Processing helix chain 'C' and resid 59 through 61 No H-bonds generated for 'chain 'C' and resid 59 through 61' Processing helix chain 'C' and resid 71 through 74 Processing helix chain 'C' and resid 78 through 84 removed outlier: 3.798A pdb=" N LYS C 84 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 576 removed outlier: 4.816A pdb=" N GLN D 567 " --> pdb=" O ASN D 563 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ALA D 568 " --> pdb=" O GLU D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 597 removed outlier: 3.843A pdb=" N ARG D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TRP D 597 " --> pdb=" O LEU D 593 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 61 No H-bonds generated for 'chain 'E' and resid 59 through 61' Processing helix chain 'E' and resid 78 through 83 Processing helix chain 'F' and resid 551 through 576 removed outlier: 4.366A pdb=" N GLN F 567 " --> pdb=" O ASN F 563 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ALA F 568 " --> pdb=" O GLU F 564 " (cutoff:3.500A) Processing helix chain 'F' and resid 584 through 598 Processing helix chain 'G' and resid 88 through 92 Processing helix chain 'H' and resid 63 through 66 removed outlier: 3.740A pdb=" N ARG H 66 " --> pdb=" O ARG H 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 63 through 66' Processing helix chain 'H' and resid 88 through 92 removed outlier: 3.568A pdb=" N THR H 92 " --> pdb=" O SER H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 225 through 229 Processing helix chain 'I' and resid 63 through 66 Processing helix chain 'I' and resid 88 through 92 Processing helix chain 'J' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 38 Processing sheet with id=AA2, first strand: chain 'A' and resid 159 through 160 removed outlier: 5.405A pdb=" N ASN A 69 " --> pdb=" O GLU A 103 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 89 Processing sheet with id=AA4, first strand: chain 'A' and resid 165 through 167 removed outlier: 6.646A pdb=" N VAL A 96 " --> pdb=" O THR B 581 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 135 through 139 removed outlier: 7.104A pdb=" N GLU A 106 " --> pdb=" O CYS A 135 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR A 137 " --> pdb=" O GLU A 106 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 36 through 38 Processing sheet with id=AA7, first strand: chain 'C' and resid 63 through 69 removed outlier: 6.010A pdb=" N GLU C 178 " --> pdb=" O ASN C 107 " (cutoff:3.500A) removed outlier: 9.158A pdb=" N ASN C 107 " --> pdb=" O GLU C 178 " (cutoff:3.500A) removed outlier: 13.765A pdb=" N VAL C 180 " --> pdb=" O ALA C 105 " (cutoff:3.500A) removed outlier: 12.241A pdb=" N ALA C 105 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLU C 106 " --> pdb=" O CYS C 135 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY C 143 " --> pdb=" O GLU C 112 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 63 through 69 removed outlier: 6.700A pdb=" N VAL C 96 " --> pdb=" O THR D 581 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 86 through 89 Processing sheet with id=AB1, first strand: chain 'C' and resid 101 through 103 Processing sheet with id=AB2, first strand: chain 'E' and resid 159 through 160 removed outlier: 3.947A pdb=" N GLU E 103 " --> pdb=" O GLY E 67 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N ASN E 69 " --> pdb=" O GLU E 103 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 86 through 89 removed outlier: 3.543A pdb=" N PHE E 151 " --> pdb=" O ARG E 89 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 166 through 167 removed outlier: 7.464A pdb=" N VAL E 96 " --> pdb=" O THR F 581 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 108 through 111 removed outlier: 7.002A pdb=" N CYS E 108 " --> pdb=" O HIS E 139 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N VAL E 141 " --> pdb=" O CYS E 108 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ASN E 110 " --> pdb=" O VAL E 141 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'G' and resid 10 through 11 removed outlier: 3.621A pdb=" N VAL G 117 " --> pdb=" O GLU G 10 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE G 34 " --> pdb=" O VAL G 50 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N VAL G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 18 through 23 removed outlier: 3.723A pdb=" N THR G 79 " --> pdb=" O ASP G 74 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 145 through 147 removed outlier: 4.285A pdb=" N GLU G 158 " --> pdb=" O VAL G 224 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ALA G 160 " --> pdb=" O SER G 222 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N SER G 222 " --> pdb=" O ALA G 160 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ILE G 162 " --> pdb=" O LYS G 220 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N LYS G 220 " --> pdb=" O ILE G 162 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N CYS G 164 " --> pdb=" O THR G 218 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N THR G 218 " --> pdb=" O CYS G 164 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N SER G 166 " --> pdb=" O ASP G 216 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ASP G 216 " --> pdb=" O SER G 166 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP G 216 " --> pdb=" O SER G 213 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER G 209 " --> pdb=" O LYS G 220 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 199 through 200 removed outlier: 6.524A pdb=" N TRP G 181 " --> pdb=" O LEU G 193 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N TYR G 195 " --> pdb=" O VAL G 179 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL G 179 " --> pdb=" O TYR G 195 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 5 through 6 removed outlier: 3.550A pdb=" N VAL H 80 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.810A pdb=" N GLU H 10 " --> pdb=" O VAL H 117 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N TYR H 32 " --> pdb=" O ASN H 52 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ASN H 52 " --> pdb=" O TYR H 32 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ILE H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N VAL H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N THR H 58 " --> pdb=" O ASN H 52 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.810A pdb=" N GLU H 10 " --> pdb=" O VAL H 117 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 145 through 147 removed outlier: 3.577A pdb=" N SER H 209 " --> pdb=" O LYS H 220 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 199 through 200 removed outlier: 6.816A pdb=" N TRP H 181 " --> pdb=" O LEU H 193 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE H 231 " --> pdb=" O GLN H 184 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AC7, first strand: chain 'I' and resid 10 through 11 removed outlier: 6.575A pdb=" N GLU I 10 " --> pdb=" O VAL I 117 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'I' and resid 59 through 61 removed outlier: 6.527A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N VAL I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ILE I 34 " --> pdb=" O VAL I 50 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG I 99 " --> pdb=" O VAL I 110 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N VAL I 110 " --> pdb=" O ARG I 99 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 145 through 147 Processing sheet with id=AD1, first strand: chain 'I' and resid 199 through 200 removed outlier: 6.548A pdb=" N TRP I 181 " --> pdb=" O LEU I 193 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N TYR I 195 " --> pdb=" O VAL I 179 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N VAL I 179 " --> pdb=" O TYR I 195 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 4 through 6 Processing sheet with id=AD3, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.394A pdb=" N GLU J 10 " --> pdb=" O THR J 121 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY J 50 " --> pdb=" O HIS J 59 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 4 through 6 Processing sheet with id=AD5, first strand: chain 'K' and resid 12 through 13 removed outlier: 3.760A pdb=" N ALA K 13 " --> pdb=" O GLU K 111 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N PHE K 39 " --> pdb=" O SER K 55 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N SER K 55 " --> pdb=" O PHE K 39 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP K 41 " --> pdb=" O LEU K 53 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 12 through 13 removed outlier: 3.760A pdb=" N ALA K 13 " --> pdb=" O GLU K 111 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N THR K 103 " --> pdb=" O GLN K 96 " (cutoff:3.500A) 422 hydrogen bonds defined for protein. 1053 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: 4.07 Time building geometry restraints manager: 5.81 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: 4136 1.34 - 1.46: 3304 1.46 - 1.58: 5619 1.58 - 1.71: 0 1.71 - 1.83: 75 Bond restraints: 13134 Sorted by residual: bond pdb=" CB PRO G 41 " pdb=" CG PRO G 41 " ideal model delta sigma weight residual 1.492 1.580 -0.088 5.00e-02 4.00e+02 3.12e+00 bond pdb=" CG1 ILE K 81 " pdb=" CD1 ILE K 81 " ideal model delta sigma weight residual 1.513 1.447 0.066 3.90e-02 6.57e+02 2.83e+00 bond pdb=" CB ASN I 174 " pdb=" CG ASN I 174 " ideal model delta sigma weight residual 1.516 1.477 0.039 2.50e-02 1.60e+03 2.41e+00 bond pdb=" CB TRP J 114 " pdb=" CG TRP J 114 " ideal model delta sigma weight residual 1.498 1.451 0.047 3.10e-02 1.04e+03 2.31e+00 bond pdb=" CB PRO I 159 " pdb=" CG PRO I 159 " ideal model delta sigma weight residual 1.492 1.567 -0.075 5.00e-02 4.00e+02 2.26e+00 ... (remaining 13129 not shown) Histogram of bond angle deviations from ideal: 99.14 - 106.14: 371 106.14 - 113.13: 7071 113.13 - 120.12: 4383 120.12 - 127.11: 5842 127.11 - 134.11: 168 Bond angle restraints: 17835 Sorted by residual: angle pdb=" CB ARG K 18 " pdb=" CG ARG K 18 " pdb=" CD ARG K 18 " ideal model delta sigma weight residual 111.30 121.35 -10.05 2.30e+00 1.89e-01 1.91e+01 angle pdb=" CA PRO G 41 " pdb=" N PRO G 41 " pdb=" CD PRO G 41 " ideal model delta sigma weight residual 112.00 106.45 5.55 1.40e+00 5.10e-01 1.57e+01 angle pdb=" C ARG G 66 " pdb=" N ASP G 67 " pdb=" CA ASP G 67 " ideal model delta sigma weight residual 121.54 129.08 -7.54 1.91e+00 2.74e-01 1.56e+01 angle pdb=" N ILE B 542 " pdb=" CA ILE B 542 " pdb=" C ILE B 542 " ideal model delta sigma weight residual 111.77 108.21 3.56 1.04e+00 9.25e-01 1.17e+01 angle pdb=" CA LEU A 57 " pdb=" CB LEU A 57 " pdb=" CG LEU A 57 " ideal model delta sigma weight residual 116.30 126.25 -9.95 3.50e+00 8.16e-02 8.09e+00 ... (remaining 17830 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.41: 7274 22.41 - 44.81: 489 44.81 - 67.22: 36 67.22 - 89.63: 39 89.63 - 112.04: 16 Dihedral angle restraints: 7854 sinusoidal: 3190 harmonic: 4664 Sorted by residual: dihedral pdb=" CB CYS G 22 " pdb=" SG CYS G 22 " pdb=" SG CYS G 97 " pdb=" CB CYS G 97 " ideal model delta sinusoidal sigma weight residual 93.00 161.39 -68.39 1 1.00e+01 1.00e-02 6.06e+01 dihedral pdb=" CB CYS K 23 " pdb=" SG CYS K 23 " pdb=" SG CYS K 94 " pdb=" CB CYS K 94 " ideal model delta sinusoidal sigma weight residual 93.00 156.93 -63.93 1 1.00e+01 1.00e-02 5.38e+01 dihedral pdb=" CB CYS I 164 " pdb=" SG CYS I 164 " pdb=" SG CYS I 234 " pdb=" CB CYS I 234 " ideal model delta sinusoidal sigma weight residual 93.00 130.18 -37.18 1 1.00e+01 1.00e-02 1.95e+01 ... (remaining 7851 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.132: 1962 0.132 - 0.264: 18 0.264 - 0.396: 3 0.396 - 0.528: 0 0.528 - 0.660: 2 Chirality restraints: 1985 Sorted by residual: chirality pdb=" C1 NAG L 1 " pdb=" ND2 ASN B 563 " pdb=" C2 NAG L 1 " pdb=" O5 NAG L 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.74 -0.66 2.00e-01 2.50e+01 1.09e+01 chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN D 563 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.80 -0.60 2.00e-01 2.50e+01 9.14e+00 chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN F 563 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.35e+00 ... (remaining 1982 not shown) Planarity restraints: 2285 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA G 40 " -0.073 5.00e-02 4.00e+02 1.09e-01 1.88e+01 pdb=" N PRO G 41 " 0.188 5.00e-02 4.00e+02 pdb=" CA PRO G 41 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO G 41 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU I 158 " -0.056 5.00e-02 4.00e+02 8.37e-02 1.12e+01 pdb=" N PRO I 159 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO I 159 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO I 159 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 115 " 0.050 5.00e-02 4.00e+02 7.57e-02 9.17e+00 pdb=" N PRO C 116 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO C 116 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 116 " 0.042 5.00e-02 4.00e+02 ... (remaining 2282 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 281 2.68 - 3.23: 12358 3.23 - 3.79: 19756 3.79 - 4.34: 26012 4.34 - 4.90: 44123 Nonbonded interactions: 102530 Sorted by model distance: nonbonded pdb=" O6 NAG N 1 " pdb=" O7 NAG N 2 " model vdw 2.124 2.440 nonbonded pdb=" OG1 THR G 70 " pdb=" OE2 GLU G 83 " model vdw 2.130 2.440 nonbonded pdb=" OE2 GLU E 156 " pdb=" O3 NAG N 1 " model vdw 2.172 2.440 nonbonded pdb=" OH TYR I 195 " pdb=" O4 BMA M 3 " model vdw 2.174 2.440 nonbonded pdb=" OD1 ASN G 33 " pdb=" ND2 ASN G 52 " model vdw 2.204 2.520 ... (remaining 102525 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 38 or resid 42 through 187)) selection = (chain 'C' and (resid 33 through 38 or resid 42 through 187)) selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = (chain 'I' and resid 2 through 250) } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } 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: 1.530 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: 0.010 Extract box with map and model: 7.720 Check model and map are aligned: 0.200 Set scattering table: 0.110 Process input model: 38.330 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 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 : 0.006 0.088 13134 Z= 0.383 Angle : 0.766 10.052 17835 Z= 0.398 Chirality : 0.053 0.660 1985 Planarity : 0.006 0.109 2282 Dihedral : 15.797 112.036 4849 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.21), residues: 1616 helix: 0.17 (0.44), residues: 141 sheet: -0.71 (0.23), residues: 540 loop : -0.58 (0.20), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP I 36 HIS 0.016 0.002 HIS F 549 PHE 0.016 0.002 PHE H 217 TYR 0.024 0.002 TYR A 99 ARG 0.027 0.002 ARG K 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 369 time to evaluate : 1.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLN cc_start: 0.7310 (pt0) cc_final: 0.6541 (mm-40) REVERT: E 100 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7556 (mm-30) REVERT: E 117 ASP cc_start: 0.7050 (m-30) cc_final: 0.6548 (p0) REVERT: F 561 LEU cc_start: 0.8826 (tp) cc_final: 0.8548 (tt) REVERT: G 36 TRP cc_start: 0.6665 (m-10) cc_final: 0.6362 (m100) REVERT: G 74 ASP cc_start: 0.7131 (m-30) cc_final: 0.6893 (m-30) REVERT: H 168 GLN cc_start: 0.8146 (tm130) cc_final: 0.7933 (tm-30) REVERT: K 80 THR cc_start: 0.8775 (m) cc_final: 0.8551 (m) REVERT: K 96 GLN cc_start: 0.8063 (pp30) cc_final: 0.7766 (pp30) outliers start: 0 outliers final: 0 residues processed: 369 average time/residue: 0.2525 time to fit residues: 132.1950 Evaluate side-chains 285 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 285 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 6.9990 chunk 121 optimal weight: 0.6980 chunk 67 optimal weight: 0.6980 chunk 41 optimal weight: 0.0970 chunk 81 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 125 optimal weight: 0.1980 chunk 48 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 chunk 145 optimal weight: 10.0000 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** D 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 174 ASN K 85 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13134 Z= 0.194 Angle : 0.633 8.759 17835 Z= 0.313 Chirality : 0.046 0.246 1985 Planarity : 0.005 0.065 2282 Dihedral : 9.841 86.037 1985 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.68 % Allowed : 11.29 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.21), residues: 1616 helix: 0.43 (0.45), residues: 141 sheet: -0.54 (0.22), residues: 557 loop : -0.58 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP I 36 HIS 0.007 0.001 HIS I 35 PHE 0.031 0.002 PHE G 96 TYR 0.013 0.001 TYR B 543 ARG 0.005 0.000 ARG G 223 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 350 time to evaluate : 1.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLN cc_start: 0.7255 (pt0) cc_final: 0.6539 (mm-40) REVERT: A 112 GLU cc_start: 0.7481 (pt0) cc_final: 0.7278 (pt0) REVERT: E 117 ASP cc_start: 0.7078 (m-30) cc_final: 0.6519 (p0) REVERT: F 561 LEU cc_start: 0.8687 (tp) cc_final: 0.8469 (tt) REVERT: G 83 GLU cc_start: 0.6766 (tm-30) cc_final: 0.6535 (tm-30) REVERT: I 13 LYS cc_start: 0.7905 (tppt) cc_final: 0.7646 (tppt) REVERT: J 46 GLU cc_start: 0.7052 (pt0) cc_final: 0.6347 (pt0) outliers start: 23 outliers final: 18 residues processed: 357 average time/residue: 0.2455 time to fit residues: 126.2913 Evaluate side-chains 315 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 297 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain D residue 592 PHE Chi-restraints excluded: chain F residue 544 THR Chi-restraints excluded: chain F residue 549 HIS Chi-restraints excluded: chain F residue 576 THR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 227 GLU Chi-restraints excluded: chain H residue 33 ASN Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 239 GLN Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 54 TYR Chi-restraints excluded: chain I residue 91 ASP Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 104 TRP Chi-restraints excluded: chain J residue 116 GLN Chi-restraints excluded: chain K residue 20 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 10.0000 chunk 45 optimal weight: 0.9980 chunk 120 optimal weight: 0.0870 chunk 98 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 chunk 145 optimal weight: 0.6980 chunk 157 optimal weight: 9.9990 chunk 129 optimal weight: 9.9990 chunk 144 optimal weight: 6.9990 chunk 49 optimal weight: 9.9990 chunk 116 optimal weight: 9.9990 overall best weight: 2.5562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS B 521 GLN C 188 GLN ** D 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 110 ASN ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 168 GLN ** H 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 174 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 13134 Z= 0.367 Angle : 0.676 11.510 17835 Z= 0.340 Chirality : 0.047 0.253 1985 Planarity : 0.005 0.057 2282 Dihedral : 8.358 78.344 1985 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 3.86 % Allowed : 16.31 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.02 (0.21), residues: 1616 helix: 0.45 (0.47), residues: 135 sheet: -0.72 (0.22), residues: 562 loop : -0.76 (0.20), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 531 HIS 0.010 0.002 HIS I 35 PHE 0.018 0.002 PHE B 592 TYR 0.017 0.002 TYR C 162 ARG 0.004 0.001 ARG G 68 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 294 time to evaluate : 1.564 Fit side-chains revert: symmetry clash REVERT: B 595 GLN cc_start: 0.7596 (pt0) cc_final: 0.7257 (tp40) REVERT: E 100 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7765 (mm-30) REVERT: E 117 ASP cc_start: 0.7163 (m-30) cc_final: 0.6604 (p0) REVERT: F 561 LEU cc_start: 0.8883 (tp) cc_final: 0.8643 (tt) REVERT: G 36 TRP cc_start: 0.7700 (m100) cc_final: 0.7047 (m100) REVERT: I 19 LYS cc_start: 0.7357 (tptt) cc_final: 0.7114 (tptt) REVERT: I 233 TYR cc_start: 0.7832 (m-10) cc_final: 0.7444 (m-10) outliers start: 53 outliers final: 45 residues processed: 319 average time/residue: 0.2449 time to fit residues: 111.9012 Evaluate side-chains 327 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 282 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 147 CYS Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 188 GLN Chi-restraints excluded: chain D residue 592 PHE Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain F residue 527 ILE Chi-restraints excluded: chain F residue 544 THR Chi-restraints excluded: chain F residue 549 HIS Chi-restraints excluded: chain F residue 583 SER Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain G residue 142 ASP Chi-restraints excluded: chain G residue 144 VAL Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 227 GLU Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain H residue 33 ASN Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 54 TYR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 87 LEU Chi-restraints excluded: chain I residue 91 ASP Chi-restraints excluded: chain I residue 109 ASP Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain K residue 9 ASP Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 66 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 97 optimal weight: 6.9990 chunk 146 optimal weight: 4.9990 chunk 154 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 138 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS B 521 GLN C 188 GLN ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 549 HIS ** H 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 174 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 13134 Z= 0.309 Angle : 0.641 8.250 17835 Z= 0.320 Chirality : 0.046 0.240 1985 Planarity : 0.005 0.056 2282 Dihedral : 7.458 72.075 1985 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 4.88 % Allowed : 18.21 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.08 (0.21), residues: 1616 helix: 0.44 (0.48), residues: 135 sheet: -0.80 (0.21), residues: 608 loop : -0.74 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP E 104 HIS 0.007 0.001 HIS I 35 PHE 0.019 0.002 PHE H 217 TYR 0.016 0.002 TYR C 162 ARG 0.006 0.001 ARG G 207 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 296 time to evaluate : 1.712 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 GLN cc_start: 0.8624 (pp30) cc_final: 0.6952 (mm-40) REVERT: B 595 GLN cc_start: 0.7631 (pt0) cc_final: 0.7168 (tp40) REVERT: E 117 ASP cc_start: 0.7247 (m-30) cc_final: 0.6621 (p0) REVERT: F 561 LEU cc_start: 0.8880 (tp) cc_final: 0.8675 (tt) REVERT: G 36 TRP cc_start: 0.7699 (m100) cc_final: 0.7142 (m100) REVERT: G 249 LYS cc_start: 0.6643 (tmtt) cc_final: 0.6368 (tmmt) REVERT: H 82 MET cc_start: 0.7485 (ttt) cc_final: 0.7277 (ttt) REVERT: K 37 ASP cc_start: 0.7212 (p0) cc_final: 0.6906 (p0) REVERT: K 89 VAL cc_start: 0.7845 (OUTLIER) cc_final: 0.7634 (p) outliers start: 67 outliers final: 53 residues processed: 334 average time/residue: 0.2331 time to fit residues: 113.0392 Evaluate side-chains 335 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 281 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain B residue 506 ASN Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 132 PHE Chi-restraints excluded: chain C residue 147 CYS Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain D residue 514 ASN Chi-restraints excluded: chain D residue 576 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain F residue 527 ILE Chi-restraints excluded: chain F residue 544 THR Chi-restraints excluded: chain F residue 549 HIS Chi-restraints excluded: chain F residue 576 THR Chi-restraints excluded: chain F residue 583 SER Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 174 ASN Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 227 GLU Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain H residue 33 ASN Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain H residue 152 LEU Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 239 GLN Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 54 TYR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 87 LEU Chi-restraints excluded: chain I residue 109 ASP Chi-restraints excluded: chain I residue 209 SER Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 116 GLN Chi-restraints excluded: chain K residue 9 ASP Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 89 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 115 optimal weight: 2.9990 chunk 63 optimal weight: 0.4980 chunk 131 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 7.9990 chunk 138 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS B 521 GLN C 188 GLN ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 174 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 13134 Z= 0.333 Angle : 0.660 12.381 17835 Z= 0.328 Chirality : 0.046 0.222 1985 Planarity : 0.005 0.056 2282 Dihedral : 7.019 66.165 1985 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 5.39 % Allowed : 18.65 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.12 (0.21), residues: 1616 helix: 0.40 (0.48), residues: 135 sheet: -0.83 (0.21), residues: 608 loop : -0.78 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP I 36 HIS 0.012 0.002 HIS F 549 PHE 0.022 0.002 PHE I 65 TYR 0.018 0.002 TYR C 162 ARG 0.006 0.001 ARG K 18 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 287 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLN cc_start: 0.8521 (pp30) cc_final: 0.6907 (mm-40) REVERT: B 595 GLN cc_start: 0.7545 (pt0) cc_final: 0.7087 (tp-100) REVERT: E 117 ASP cc_start: 0.7368 (m-30) cc_final: 0.6659 (p0) REVERT: F 561 LEU cc_start: 0.8900 (tp) cc_final: 0.8667 (tt) REVERT: G 36 TRP cc_start: 0.8012 (m100) cc_final: 0.7537 (m100) REVERT: G 249 LYS cc_start: 0.6708 (tmtt) cc_final: 0.6451 (tmmt) REVERT: H 82 MET cc_start: 0.7448 (ttt) cc_final: 0.7226 (ttt) REVERT: K 37 ASP cc_start: 0.7201 (p0) cc_final: 0.6942 (p0) REVERT: K 89 VAL cc_start: 0.7821 (OUTLIER) cc_final: 0.7608 (p) outliers start: 74 outliers final: 64 residues processed: 326 average time/residue: 0.2372 time to fit residues: 111.3184 Evaluate side-chains 339 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 274 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain B residue 506 ASN Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 132 PHE Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 147 CYS Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 188 GLN Chi-restraints excluded: chain D residue 514 ASN Chi-restraints excluded: chain D residue 545 GLU Chi-restraints excluded: chain D residue 573 LEU Chi-restraints excluded: chain D residue 576 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain F residue 527 ILE Chi-restraints excluded: chain F residue 544 THR Chi-restraints excluded: chain F residue 549 HIS Chi-restraints excluded: chain F residue 583 SER Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain G residue 142 ASP Chi-restraints excluded: chain G residue 144 VAL Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 174 ASN Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 227 GLU Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain H residue 33 ASN Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 152 LEU Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 54 TYR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 87 LEU Chi-restraints excluded: chain I residue 91 ASP Chi-restraints excluded: chain I residue 109 ASP Chi-restraints excluded: chain I residue 209 SER Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 116 GLN Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 9 ASP Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 89 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 4.9990 chunk 139 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 90 optimal weight: 9.9990 chunk 38 optimal weight: 0.9980 chunk 154 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 71 optimal weight: 7.9990 chunk 12 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS B 521 GLN C 188 GLN ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 174 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 13134 Z= 0.260 Angle : 0.635 8.835 17835 Z= 0.315 Chirality : 0.045 0.212 1985 Planarity : 0.005 0.055 2282 Dihedral : 6.636 60.844 1985 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 4.59 % Allowed : 21.12 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.09 (0.21), residues: 1616 helix: 0.51 (0.48), residues: 135 sheet: -0.83 (0.21), residues: 607 loop : -0.75 (0.21), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP I 36 HIS 0.005 0.001 HIS B 516 PHE 0.018 0.002 PHE G 96 TYR 0.016 0.001 TYR C 162 ARG 0.003 0.000 ARG K 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 292 time to evaluate : 1.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLN cc_start: 0.8485 (pp30) cc_final: 0.6864 (mm-40) REVERT: B 595 GLN cc_start: 0.7577 (pt0) cc_final: 0.7015 (tp-100) REVERT: E 117 ASP cc_start: 0.7372 (m-30) cc_final: 0.6673 (p0) REVERT: F 561 LEU cc_start: 0.8875 (tp) cc_final: 0.8654 (tt) REVERT: G 18 VAL cc_start: 0.7981 (t) cc_final: 0.7690 (m) REVERT: G 249 LYS cc_start: 0.6647 (tmtt) cc_final: 0.6414 (tmmt) REVERT: H 96 PHE cc_start: 0.8488 (m-80) cc_final: 0.8135 (m-10) REVERT: K 37 ASP cc_start: 0.7212 (p0) cc_final: 0.6955 (p0) REVERT: K 89 VAL cc_start: 0.7772 (OUTLIER) cc_final: 0.7565 (p) outliers start: 63 outliers final: 55 residues processed: 329 average time/residue: 0.2426 time to fit residues: 115.1014 Evaluate side-chains 337 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 281 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain B residue 506 ASN Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 132 PHE Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain D residue 514 ASN Chi-restraints excluded: chain D residue 545 GLU Chi-restraints excluded: chain D residue 573 LEU Chi-restraints excluded: chain D residue 576 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain F residue 527 ILE Chi-restraints excluded: chain F residue 544 THR Chi-restraints excluded: chain F residue 549 HIS Chi-restraints excluded: chain F residue 583 SER Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 174 ASN Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 227 GLU Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain H residue 33 ASN Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 152 LEU Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 54 TYR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 87 LEU Chi-restraints excluded: chain I residue 109 ASP Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 9 ASP Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 89 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 7.9990 chunk 17 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 113 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 154 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 40 ASN B 521 GLN C 188 GLN ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 174 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 13134 Z= 0.300 Angle : 0.653 11.609 17835 Z= 0.323 Chirality : 0.045 0.193 1985 Planarity : 0.005 0.056 2282 Dihedral : 6.409 55.046 1985 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 5.32 % Allowed : 21.70 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.15 (0.21), residues: 1616 helix: 0.05 (0.46), residues: 149 sheet: -0.75 (0.22), residues: 581 loop : -0.84 (0.20), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 104 HIS 0.005 0.001 HIS B 516 PHE 0.017 0.002 PHE H 29 TYR 0.015 0.001 TYR C 162 ARG 0.005 0.000 ARG K 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 286 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 GLN cc_start: 0.8502 (pp30) cc_final: 0.6848 (mm-40) REVERT: A 63 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7888 (mt) REVERT: C 113 ILE cc_start: 0.8182 (OUTLIER) cc_final: 0.7977 (pt) REVERT: E 117 ASP cc_start: 0.7390 (m-30) cc_final: 0.6693 (p0) REVERT: F 561 LEU cc_start: 0.8887 (tp) cc_final: 0.8642 (tt) REVERT: G 249 LYS cc_start: 0.6642 (tmtt) cc_final: 0.6415 (tmmt) REVERT: H 96 PHE cc_start: 0.8557 (OUTLIER) cc_final: 0.7939 (m-10) REVERT: I 36 TRP cc_start: 0.8071 (m100) cc_final: 0.7740 (m100) REVERT: I 71 MET cc_start: 0.7529 (mtp) cc_final: 0.7058 (mtt) REVERT: I 82 MET cc_start: 0.7419 (OUTLIER) cc_final: 0.6878 (mtm) REVERT: K 37 ASP cc_start: 0.7154 (p0) cc_final: 0.6856 (p0) REVERT: K 89 VAL cc_start: 0.7772 (OUTLIER) cc_final: 0.7566 (p) outliers start: 73 outliers final: 61 residues processed: 327 average time/residue: 0.2408 time to fit residues: 114.2587 Evaluate side-chains 337 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 271 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain B residue 506 ASN Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 132 PHE Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 188 GLN Chi-restraints excluded: chain D residue 514 ASN Chi-restraints excluded: chain D residue 545 GLU Chi-restraints excluded: chain D residue 573 LEU Chi-restraints excluded: chain D residue 576 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain F residue 527 ILE Chi-restraints excluded: chain F residue 544 THR Chi-restraints excluded: chain F residue 549 HIS Chi-restraints excluded: chain F residue 583 SER Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 164 CYS Chi-restraints excluded: chain G residue 174 ASN Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 227 GLU Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain H residue 33 ASN Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 96 PHE Chi-restraints excluded: chain H residue 152 LEU Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 54 TYR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 82 MET Chi-restraints excluded: chain I residue 87 LEU Chi-restraints excluded: chain I residue 91 ASP Chi-restraints excluded: chain I residue 109 ASP Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 116 GLN Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 89 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 105 optimal weight: 0.2980 chunk 76 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 121 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 40 ASN B 521 GLN B 551 GLN ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 174 ASN J 103 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 13134 Z= 0.199 Angle : 0.634 9.029 17835 Z= 0.313 Chirality : 0.044 0.204 1985 Planarity : 0.005 0.060 2282 Dihedral : 5.854 51.535 1985 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.86 % Allowed : 23.45 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.02 (0.21), residues: 1616 helix: 0.65 (0.49), residues: 135 sheet: -0.77 (0.22), residues: 575 loop : -0.75 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 104 HIS 0.005 0.001 HIS B 516 PHE 0.018 0.001 PHE G 96 TYR 0.012 0.001 TYR C 162 ARG 0.005 0.000 ARG J 87 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 299 time to evaluate : 1.415 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 GLN cc_start: 0.8512 (pp30) cc_final: 0.6877 (mm-40) REVERT: A 63 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7847 (mt) REVERT: A 99 TYR cc_start: 0.9030 (p90) cc_final: 0.8593 (p90) REVERT: C 113 ILE cc_start: 0.8062 (OUTLIER) cc_final: 0.7757 (pt) REVERT: E 117 ASP cc_start: 0.7424 (m-30) cc_final: 0.6715 (p0) REVERT: H 96 PHE cc_start: 0.8421 (m-80) cc_final: 0.8026 (m-10) REVERT: I 36 TRP cc_start: 0.7955 (m100) cc_final: 0.7580 (m100) REVERT: I 82 MET cc_start: 0.7326 (OUTLIER) cc_final: 0.6267 (mtm) REVERT: J 67 ARG cc_start: 0.6431 (ptm-80) cc_final: 0.6225 (ptp-170) REVERT: K 37 ASP cc_start: 0.7001 (p0) cc_final: 0.6703 (p0) REVERT: K 42 TYR cc_start: 0.8852 (m-10) cc_final: 0.8636 (m-80) REVERT: K 89 VAL cc_start: 0.7826 (OUTLIER) cc_final: 0.7624 (p) outliers start: 53 outliers final: 37 residues processed: 332 average time/residue: 0.2465 time to fit residues: 118.5629 Evaluate side-chains 322 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 281 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain B residue 506 ASN Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 551 GLN Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 132 PHE Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain D residue 573 LEU Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain F residue 544 THR Chi-restraints excluded: chain F residue 549 HIS Chi-restraints excluded: chain F residue 583 SER Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 174 ASN Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 227 GLU Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain H residue 33 ASN Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 152 LEU Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 54 TYR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 82 MET Chi-restraints excluded: chain I residue 109 ASP Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 89 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 134 optimal weight: 0.0870 chunk 143 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 112 optimal weight: 8.9990 chunk 44 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 chunk 135 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 overall best weight: 1.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 40 ASN B 551 GLN ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 508 GLN ** F 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 168 GLN I 174 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 13134 Z= 0.231 Angle : 0.644 8.913 17835 Z= 0.317 Chirality : 0.045 0.193 1985 Planarity : 0.005 0.056 2282 Dihedral : 5.696 50.972 1985 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.64 % Allowed : 24.25 % Favored : 72.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.21), residues: 1616 helix: 0.66 (0.48), residues: 135 sheet: -0.80 (0.21), residues: 609 loop : -0.72 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP E 104 HIS 0.010 0.001 HIS I 35 PHE 0.025 0.002 PHE G 96 TYR 0.019 0.001 TYR H 233 ARG 0.005 0.000 ARG K 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 285 time to evaluate : 1.474 Fit side-chains revert: symmetry clash REVERT: A 62 GLN cc_start: 0.8427 (pp30) cc_final: 0.6781 (mm-40) REVERT: A 63 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7814 (mt) REVERT: A 99 TYR cc_start: 0.9026 (p90) cc_final: 0.8601 (p90) REVERT: E 117 ASP cc_start: 0.7406 (m-30) cc_final: 0.6694 (p0) REVERT: H 96 PHE cc_start: 0.8509 (m-80) cc_final: 0.8012 (m-10) REVERT: J 67 ARG cc_start: 0.6548 (ptm-80) cc_final: 0.6269 (ptp-170) REVERT: K 37 ASP cc_start: 0.7010 (p0) cc_final: 0.6718 (p0) REVERT: K 42 TYR cc_start: 0.8863 (m-10) cc_final: 0.8646 (m-80) REVERT: K 89 VAL cc_start: 0.7841 (OUTLIER) cc_final: 0.7637 (p) outliers start: 50 outliers final: 40 residues processed: 317 average time/residue: 0.2385 time to fit residues: 109.1455 Evaluate side-chains 322 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 280 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain B residue 506 ASN Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 551 GLN Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 132 PHE Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 147 CYS Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain D residue 514 ASN Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 573 LEU Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain F residue 527 ILE Chi-restraints excluded: chain F residue 544 THR Chi-restraints excluded: chain F residue 549 HIS Chi-restraints excluded: chain F residue 583 SER Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain G residue 174 ASN Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 227 GLU Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain H residue 33 ASN Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 152 LEU Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 54 TYR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 109 ASP Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 89 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 159 optimal weight: 0.5980 chunk 146 optimal weight: 0.6980 chunk 126 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 40 ASN B 551 GLN ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 GLN ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 521 GLN ** G 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 168 GLN ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 174 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 13134 Z= 0.206 Angle : 0.657 10.794 17835 Z= 0.319 Chirality : 0.044 0.198 1985 Planarity : 0.005 0.057 2282 Dihedral : 5.509 51.952 1985 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.28 % Allowed : 24.69 % Favored : 72.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.21), residues: 1616 helix: 0.69 (0.48), residues: 135 sheet: -0.74 (0.22), residues: 576 loop : -0.72 (0.20), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP E 104 HIS 0.011 0.001 HIS I 35 PHE 0.024 0.001 PHE G 96 TYR 0.019 0.001 TYR H 54 ARG 0.005 0.000 ARG K 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 282 time to evaluate : 1.579 Fit side-chains revert: symmetry clash REVERT: A 62 GLN cc_start: 0.8395 (pp30) cc_final: 0.6837 (mm-40) REVERT: A 63 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7787 (mt) REVERT: A 99 TYR cc_start: 0.8974 (p90) cc_final: 0.8657 (p90) REVERT: E 117 ASP cc_start: 0.7407 (m-30) cc_final: 0.6645 (p0) REVERT: G 18 VAL cc_start: 0.7958 (t) cc_final: 0.7575 (m) REVERT: G 36 TRP cc_start: 0.7954 (m100) cc_final: 0.7385 (m100) REVERT: H 96 PHE cc_start: 0.8500 (m-80) cc_final: 0.7989 (m-10) REVERT: I 36 TRP cc_start: 0.7752 (m100) cc_final: 0.7428 (m-10) REVERT: I 82 MET cc_start: 0.7137 (OUTLIER) cc_final: 0.5781 (mtm) REVERT: J 67 ARG cc_start: 0.6516 (ptm-80) cc_final: 0.6172 (ptp-170) REVERT: K 37 ASP cc_start: 0.6993 (p0) cc_final: 0.6718 (p0) outliers start: 45 outliers final: 40 residues processed: 311 average time/residue: 0.2512 time to fit residues: 112.8427 Evaluate side-chains 312 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 270 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain B residue 506 ASN Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 551 GLN Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 132 PHE Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 147 CYS Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 188 GLN Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 573 LEU Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain F residue 544 THR Chi-restraints excluded: chain F residue 549 HIS Chi-restraints excluded: chain F residue 583 SER Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 174 ASN Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 227 GLU Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain H residue 33 ASN Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 152 LEU Chi-restraints excluded: chain H residue 239 GLN Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 54 TYR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 82 MET Chi-restraints excluded: chain I residue 109 ASP Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain K residue 20 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 9.9990 chunk 38 optimal weight: 0.6980 chunk 117 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 16 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 111 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 40 ASN ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 168 GLN ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 174 ASN ** K 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.125454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.106048 restraints weight = 27725.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.109291 restraints weight = 15416.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.111519 restraints weight = 10459.911| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 13134 Z= 0.216 Angle : 0.653 9.234 17835 Z= 0.319 Chirality : 0.044 0.194 1985 Planarity : 0.005 0.056 2282 Dihedral : 5.440 51.613 1985 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.50 % Allowed : 23.89 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.21), residues: 1616 helix: 0.75 (0.48), residues: 135 sheet: -0.76 (0.22), residues: 578 loop : -0.71 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP E 104 HIS 0.009 0.001 HIS I 35 PHE 0.024 0.002 PHE G 96 TYR 0.016 0.001 TYR J 32 ARG 0.008 0.000 ARG E 89 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3040.01 seconds wall clock time: 55 minutes 29.02 seconds (3329.02 seconds total)