Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 16:57:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swd_25471/04_2023/7swd_25471.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swd_25471/04_2023/7swd_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_25471/04_2023/7swd_25471.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swd_25471/04_2023/7swd_25471.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swd_25471/04_2023/7swd_25471.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swd_25471/04_2023/7swd_25471.pdb" } resolution = 3.59 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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 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 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 chiralities: 3 Time building chain proxies: 7.00, per 1000 atoms: 0.55 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 1.9 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: 0.87 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: 4.10 Time building geometry restraints manager: 5.80 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 - 17.29: 6928 17.29 - 34.59: 606 34.59 - 51.88: 104 51.88 - 69.18: 20 69.18 - 86.47: 13 Dihedral angle restraints: 7671 sinusoidal: 3007 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 7668 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: 1.410 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: 8.130 Check model and map are aligned: 0.200 Set scattering table: 0.110 Process input model: 34.930 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.730 ------------------------------------------------------------------------------- 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 : 13.467 86.469 4666 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 % 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 *********************** 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 : 1.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 369 average time/residue: 0.2522 time to fit residues: 132.4847 Evaluate side-chains 280 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 280 time to evaluate : 1.402 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9305 ------------------------------------------------------------------------------- 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: 0.6980 chunk 121 optimal weight: 0.6980 chunk 67 optimal weight: 4.9990 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: 6.9990 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: 0.7805 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 13134 Z= 0.194 Angle : 0.628 8.842 17835 Z= 0.314 Chirality : 0.045 0.219 1985 Planarity : 0.005 0.065 2282 Dihedral : 4.773 22.746 1802 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer Outliers : 1.75 % 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: -0.81 (0.21), residues: 1616 helix: 0.41 (0.45), residues: 141 sheet: -0.55 (0.22), residues: 557 loop : -0.60 (0.20), residues: 918 *********************** 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 370 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 346 time to evaluate : 1.496 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 21 residues processed: 352 average time/residue: 0.2454 time to fit residues: 124.5257 Evaluate side-chains 316 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 295 time to evaluate : 1.460 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1374 time to fit residues: 7.1302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 7.9990 chunk 45 optimal weight: 0.9980 chunk 120 optimal weight: 0.8980 chunk 98 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 chunk 145 optimal weight: 0.9980 chunk 157 optimal weight: 0.0270 chunk 129 optimal weight: 10.0000 chunk 144 optimal weight: 2.9990 chunk 49 optimal weight: 9.9990 chunk 116 optimal weight: 8.9990 overall best weight: 1.1840 ------------------------------------------------------------------------------- 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 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 13134 Z= 0.224 Angle : 0.603 11.329 17835 Z= 0.301 Chirality : 0.044 0.208 1985 Planarity : 0.005 0.057 2282 Dihedral : 4.658 23.230 1802 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer Outliers : 2.26 % 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: -0.85 (0.21), residues: 1616 helix: 0.51 (0.46), residues: 141 sheet: -0.59 (0.22), residues: 562 loop : -0.65 (0.20), residues: 913 *********************** 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 351 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 320 time to evaluate : 1.421 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 21 residues processed: 336 average time/residue: 0.2623 time to fit residues: 128.5210 Evaluate side-chains 316 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 295 time to evaluate : 1.482 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1194 time to fit residues: 6.5332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 7.9990 chunk 109 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 chunk 146 optimal weight: 7.9990 chunk 154 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 138 optimal weight: 9.9990 chunk 41 optimal weight: 0.1980 overall best weight: 2.2386 ------------------------------------------------------------------------------- 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 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 549 HIS 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 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 0.071 13134 Z= 0.327 Angle : 0.647 10.227 17835 Z= 0.325 Chirality : 0.045 0.191 1985 Planarity : 0.005 0.057 2282 Dihedral : 4.836 24.558 1802 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer Outliers : 3.13 % 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: -0.97 (0.21), residues: 1616 helix: 0.52 (0.47), residues: 135 sheet: -0.75 (0.22), residues: 578 loop : -0.67 (0.20), residues: 903 *********************** 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 346 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 303 time to evaluate : 1.587 Fit side-chains revert: symmetry clash outliers start: 43 outliers final: 26 residues processed: 329 average time/residue: 0.2494 time to fit residues: 119.1880 Evaluate side-chains 309 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 283 time to evaluate : 1.430 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.1256 time to fit residues: 7.6969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 0.0060 chunk 87 optimal weight: 0.0970 chunk 2 optimal weight: 10.0000 chunk 115 optimal weight: 0.2980 chunk 63 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 8.9990 chunk 138 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 overall best weight: 1.2796 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 549 HIS G 39 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 13134 Z= 0.227 Angle : 0.609 8.641 17835 Z= 0.304 Chirality : 0.044 0.174 1985 Planarity : 0.005 0.058 2282 Dihedral : 4.679 24.683 1802 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer Outliers : 1.09 % 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: -0.96 (0.21), residues: 1616 helix: 0.57 (0.47), residues: 135 sheet: -0.73 (0.22), residues: 583 loop : -0.68 (0.20), residues: 898 *********************** 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 318 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 303 time to evaluate : 1.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 12 residues processed: 309 average time/residue: 0.2518 time to fit residues: 113.1708 Evaluate side-chains 294 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 282 time to evaluate : 1.544 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1262 time to fit residues: 4.8658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 30 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 154 optimal weight: 6.9990 chunk 128 optimal weight: 6.9990 chunk 71 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 81 optimal weight: 0.5980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 GLN ** 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 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: 0.7892 moved from start: 0.2215 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= 0.230 Angle : 0.601 7.610 17835 Z= 0.300 Chirality : 0.043 0.170 1985 Planarity : 0.005 0.057 2282 Dihedral : 4.610 24.587 1802 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer Outliers : 1.75 % 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: -0.94 (0.21), residues: 1616 helix: 0.67 (0.48), residues: 135 sheet: -0.75 (0.22), residues: 581 loop : -0.65 (0.21), residues: 900 *********************** 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 320 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 296 time to evaluate : 1.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 17 residues processed: 308 average time/residue: 0.2466 time to fit residues: 110.3013 Evaluate side-chains 294 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 277 time to evaluate : 1.514 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1398 time to fit residues: 6.0987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 88 optimal weight: 0.8980 chunk 113 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 154 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 508 GLN G 174 ASN ** H 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 174 ASN K 48 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 13134 Z= 0.256 Angle : 0.616 7.674 17835 Z= 0.309 Chirality : 0.044 0.183 1985 Planarity : 0.005 0.056 2282 Dihedral : 4.676 24.345 1802 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer Outliers : 1.24 % 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: -0.99 (0.21), residues: 1616 helix: 0.73 (0.47), residues: 135 sheet: -0.79 (0.21), residues: 611 loop : -0.68 (0.21), residues: 870 *********************** 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 309 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 292 time to evaluate : 1.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 12 residues processed: 299 average time/residue: 0.2628 time to fit residues: 114.8157 Evaluate side-chains 288 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 276 time to evaluate : 1.545 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1264 time to fit residues: 4.8871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 C 188 GLN ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 521 GLN ** H 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 174 ASN J 103 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 13134 Z= 0.202 Angle : 0.610 8.444 17835 Z= 0.303 Chirality : 0.043 0.179 1985 Planarity : 0.005 0.058 2282 Dihedral : 4.560 24.483 1802 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer Outliers : 1.38 % 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: -0.92 (0.21), residues: 1616 helix: 0.88 (0.48), residues: 135 sheet: -0.78 (0.21), residues: 612 loop : -0.63 (0.21), residues: 869 *********************** 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 312 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 293 time to evaluate : 1.540 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 11 residues processed: 303 average time/residue: 0.2516 time to fit residues: 110.1429 Evaluate side-chains 290 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 279 time to evaluate : 1.442 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1475 time to fit residues: 4.6514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 4.9990 chunk 147 optimal weight: 0.5980 chunk 134 optimal weight: 10.0000 chunk 143 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 112 optimal weight: 9.9990 chunk 44 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 chunk 135 optimal weight: 0.7980 chunk 94 optimal weight: 7.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 52 ASN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 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 0.050 13134 Z= 0.234 Angle : 0.623 7.905 17835 Z= 0.309 Chirality : 0.044 0.165 1985 Planarity : 0.005 0.057 2282 Dihedral : 4.546 24.153 1802 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer Outliers : 0.95 % 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: 0.71 (0.48), residues: 135 sheet: -0.78 (0.21), residues: 605 loop : -0.68 (0.21), residues: 876 *********************** 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 303 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 290 time to evaluate : 1.540 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 294 average time/residue: 0.2534 time to fit residues: 106.9009 Evaluate side-chains 285 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 277 time to evaluate : 1.597 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1278 time to fit residues: 3.9521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 8.9990 chunk 92 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 105 optimal weight: 0.5980 chunk 159 optimal weight: 0.9990 chunk 146 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- 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 ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 236 GLN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 13134 Z= 0.234 Angle : 0.646 11.888 17835 Z= 0.319 Chirality : 0.044 0.168 1985 Planarity : 0.005 0.064 2282 Dihedral : 4.571 24.075 1802 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer Outliers : 0.44 % 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: -0.97 (0.21), residues: 1616 helix: 0.75 (0.48), residues: 135 sheet: -0.81 (0.21), residues: 615 loop : -0.65 (0.21), residues: 866 ********************** 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 287 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 281 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 282 average time/residue: 0.2438 time to fit residues: 100.2163 Evaluate side-chains 277 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 272 time to evaluate : 1.564 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1843 time to fit residues: 3.4078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 8.9990 chunk 38 optimal weight: 9.9990 chunk 117 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 127 optimal weight: 0.0270 chunk 53 optimal weight: 0.8980 chunk 130 optimal weight: 0.9980 chunk 16 optimal weight: 0.0170 chunk 23 optimal weight: 5.9990 chunk 111 optimal weight: 0.5980 overall best weight: 0.5076 ------------------------------------------------------------------------------- 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 ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 516 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.127513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.108346 restraints weight = 27799.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.111691 restraints weight = 15301.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.113977 restraints weight = 10296.175| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 13134 Z= 0.179 Angle : 0.629 11.634 17835 Z= 0.309 Chirality : 0.043 0.178 1985 Planarity : 0.005 0.057 2282 Dihedral : 4.386 23.383 1802 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer Outliers : 0.73 % 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: -0.86 (0.21), residues: 1616 helix: 0.91 (0.48), residues: 135 sheet: -0.73 (0.21), residues: 612 loop : -0.59 (0.21), residues: 869 =============================================================================== Job complete usr+sys time: 2837.82 seconds wall clock time: 52 minutes 19.04 seconds (3139.04 seconds total)