Starting phenix.real_space_refine on Thu Sep 26 10:34:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swd_25471/09_2024/7swd_25471.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swd_25471/09_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_25471/09_2024/7swd_25471.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swd_25471/09_2024/7swd_25471.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swd_25471/09_2024/7swd_25471.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swd_25471/09_2024/7swd_25471.cif" } 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. Time to flip 22 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 8.52, per 1000 atoms: 0.66 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 - 3.00 Amino acid : True - 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: 3.61 Conformation dependent library (CDL) restraints added in 1.8 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: 1.96 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: 3.85 Time building geometry restraints manager: 4.06 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: 0.00 - 2.01: 17341 2.01 - 4.02: 430 4.02 - 6.03: 48 6.03 - 8.04: 14 8.04 - 10.05: 2 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 3.040 nonbonded pdb=" OG1 THR G 70 " pdb=" OE2 GLU G 83 " model vdw 2.130 3.040 nonbonded pdb=" OE2 GLU E 156 " pdb=" O3 NAG N 1 " model vdw 2.172 3.040 nonbonded pdb=" OH TYR I 195 " pdb=" O4 BMA M 3 " model vdw 2.174 3.040 nonbonded pdb=" OD1 ASN G 33 " pdb=" ND2 ASN G 52 " model vdw 2.204 3.120 ... (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 Time spend for trying shortcut: 0.00 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: 2.870 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: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 32.520 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.510 ------------------------------------------------------------------------------- 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 : 1.479 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: 0.2466 time to fit residues: 130.0218 Evaluate side-chains 285 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 285 time to evaluate : 1.488 ------------------------------------------------------------------------------- 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: 7.9990 chunk 121 optimal weight: 5.9990 chunk 67 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 93 optimal weight: 0.7980 chunk 145 optimal weight: 10.0000 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 85 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 13134 Z= 0.272 Angle : 0.663 8.357 17835 Z= 0.333 Chirality : 0.047 0.239 1985 Planarity : 0.006 0.066 2282 Dihedral : 10.429 87.967 1985 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.97 % Allowed : 11.58 % Favored : 86.45 % 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: -0.89 (0.21), residues: 1616 helix: 0.34 (0.45), residues: 141 sheet: -0.62 (0.22), residues: 557 loop : -0.65 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP I 36 HIS 0.009 0.001 HIS I 35 PHE 0.028 0.002 PHE G 96 TYR 0.017 0.002 TYR I 81 ARG 0.005 0.001 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 362 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 335 time to evaluate : 1.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLN cc_start: 0.7406 (pt0) cc_final: 0.6613 (mm-40) REVERT: A 112 GLU cc_start: 0.7634 (pt0) cc_final: 0.7325 (pt0) REVERT: E 117 ASP cc_start: 0.7209 (m-30) cc_final: 0.6651 (p0) REVERT: F 561 LEU cc_start: 0.8786 (tp) cc_final: 0.8507 (tt) REVERT: G 249 LYS cc_start: 0.6660 (tmtt) cc_final: 0.6367 (tmmt) REVERT: I 13 LYS cc_start: 0.7884 (tppt) cc_final: 0.7637 (tppt) REVERT: J 46 GLU cc_start: 0.7158 (pt0) cc_final: 0.6468 (pt0) REVERT: K 42 TYR cc_start: 0.9024 (m-80) cc_final: 0.8783 (m-10) REVERT: K 96 GLN cc_start: 0.8047 (pp30) cc_final: 0.7841 (pp30) outliers start: 27 outliers final: 22 residues processed: 345 average time/residue: 0.2488 time to fit residues: 123.2231 Evaluate side-chains 304 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 282 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain D residue 592 PHE Chi-restraints excluded: chain E residue 167 SER 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 72 THR Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 227 GLU 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 72 THR Chi-restraints excluded: chain I residue 91 ASP Chi-restraints excluded: chain I residue 209 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 Chi-restraints excluded: chain K residue 66 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 9.9990 chunk 45 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 chunk 98 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 145 optimal weight: 9.9990 chunk 157 optimal weight: 0.8980 chunk 129 optimal weight: 10.0000 chunk 144 optimal weight: 0.9990 chunk 49 optimal weight: 9.9990 chunk 116 optimal weight: 9.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** B 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 GLN ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 549 HIS G 52 ASN H 168 GLN ** H 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 239 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 13134 Z= 0.370 Angle : 0.683 11.365 17835 Z= 0.343 Chirality : 0.047 0.249 1985 Planarity : 0.005 0.056 2282 Dihedral : 9.024 80.824 1985 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 3.42 % Allowed : 16.10 % Favored : 80.48 % 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: -1.05 (0.21), residues: 1616 helix: 0.41 (0.46), residues: 141 sheet: -0.74 (0.22), residues: 557 loop : -0.78 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 531 HIS 0.008 0.001 HIS I 35 PHE 0.019 0.002 PHE G 96 TYR 0.018 0.002 TYR C 162 ARG 0.005 0.001 ARG A 164 *********************** 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 350 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 303 time to evaluate : 1.590 Fit side-chains revert: symmetry clash REVERT: A 62 GLN cc_start: 0.7088 (pt0) cc_final: 0.6620 (mm-40) REVERT: A 140 LYS cc_start: 0.8385 (mmmm) cc_final: 0.8101 (mmmm) REVERT: B 595 GLN cc_start: 0.7686 (pt0) cc_final: 0.7246 (tp40) REVERT: E 100 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7658 (mm-30) REVERT: E 117 ASP cc_start: 0.7216 (m-30) cc_final: 0.6627 (p0) REVERT: F 561 LEU cc_start: 0.8910 (tp) cc_final: 0.8608 (tt) REVERT: G 249 LYS cc_start: 0.6616 (tmtt) cc_final: 0.6374 (tmmt) REVERT: I 251 GLU cc_start: 0.8000 (pm20) cc_final: 0.7362 (pm20) REVERT: K 37 ASP cc_start: 0.7058 (p0) cc_final: 0.6790 (p0) REVERT: K 42 TYR cc_start: 0.9068 (m-80) cc_final: 0.8810 (m-10) REVERT: K 96 GLN cc_start: 0.8191 (pp30) cc_final: 0.7827 (pp30) outliers start: 47 outliers final: 38 residues processed: 325 average time/residue: 0.2477 time to fit residues: 115.1971 Evaluate side-chains 325 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 287 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 548 MET Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 109 TYR Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 147 CYS Chi-restraints excluded: chain C residue 188 GLN Chi-restraints excluded: chain D residue 576 THR Chi-restraints excluded: chain E residue 167 SER 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 G residue 51 ILE Chi-restraints excluded: chain G residue 72 THR 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 51 ILE Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 152 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 142 ASP Chi-restraints excluded: chain I residue 209 SER Chi-restraints excluded: chain J residue 37 VAL 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 146 optimal weight: 0.9990 chunk 154 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 138 optimal weight: 9.9990 chunk 41 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS B 516 HIS C 188 GLN ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 168 GLN ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13134 Z= 0.268 Angle : 0.639 9.108 17835 Z= 0.320 Chirality : 0.045 0.243 1985 Planarity : 0.005 0.058 2282 Dihedral : 7.914 75.475 1985 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.71 % Allowed : 18.28 % Favored : 78.00 % 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: -1.00 (0.21), residues: 1616 helix: 0.48 (0.47), residues: 135 sheet: -0.76 (0.22), residues: 572 loop : -0.70 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 36 HIS 0.011 0.001 HIS F 549 PHE 0.017 0.002 PHE G 96 TYR 0.014 0.001 TYR C 162 ARG 0.004 0.000 ARG J 67 *********************** 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 355 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 304 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLN cc_start: 0.6984 (pt0) cc_final: 0.6644 (mm-40) REVERT: B 595 GLN cc_start: 0.7566 (pt0) cc_final: 0.7115 (tp-100) REVERT: E 100 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7524 (mm-30) REVERT: E 117 ASP cc_start: 0.7377 (m-30) cc_final: 0.6647 (p0) REVERT: F 561 LEU cc_start: 0.8728 (tp) cc_final: 0.8478 (tt) REVERT: G 249 LYS cc_start: 0.6627 (tmtt) cc_final: 0.6381 (tmmt) REVERT: I 251 GLU cc_start: 0.8087 (pm20) cc_final: 0.7413 (pm20) REVERT: K 37 ASP cc_start: 0.7123 (p0) cc_final: 0.6822 (p0) REVERT: K 42 TYR cc_start: 0.9018 (m-80) cc_final: 0.8386 (m-10) REVERT: K 96 GLN cc_start: 0.8153 (pp30) cc_final: 0.7743 (pp30) outliers start: 51 outliers final: 41 residues processed: 332 average time/residue: 0.2456 time to fit residues: 117.3019 Evaluate side-chains 327 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 286 time to evaluate : 1.474 ------------------------------------------------------------------------------- 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 185 ILE Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 109 TYR Chi-restraints excluded: chain C residue 147 CYS Chi-restraints excluded: chain D residue 545 GLU Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 167 SER 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 G residue 51 ILE Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 152 LEU 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 51 ILE Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 152 LEU Chi-restraints excluded: chain H residue 239 GLN Chi-restraints excluded: chain H residue 250 VAL 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 80 VAL Chi-restraints excluded: chain I residue 87 LEU Chi-restraints excluded: chain I residue 91 ASP Chi-restraints excluded: chain I residue 142 ASP Chi-restraints excluded: chain I residue 209 SER Chi-restraints excluded: chain J residue 37 VAL 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 66 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 115 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 131 optimal weight: 0.6980 chunk 106 optimal weight: 0.0470 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 138 optimal weight: 10.0000 chunk 39 optimal weight: 0.0980 overall best weight: 0.5280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 69 ASN C 188 GLN D 508 GLN D 560 GLN ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 168 GLN ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 GLN J 103 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13134 Z= 0.181 Angle : 0.625 11.128 17835 Z= 0.307 Chirality : 0.044 0.232 1985 Planarity : 0.005 0.058 2282 Dihedral : 6.839 68.007 1985 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.62 % Allowed : 20.83 % Favored : 76.55 % 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: 0.54 (0.48), residues: 135 sheet: -0.68 (0.22), residues: 571 loop : -0.57 (0.21), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP E 104 HIS 0.005 0.001 HIS I 35 PHE 0.027 0.002 PHE I 65 TYR 0.014 0.001 TYR B 543 ARG 0.008 0.000 ARG E 134 *********************** 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 370 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 334 time to evaluate : 1.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLN cc_start: 0.6855 (pt0) cc_final: 0.6644 (mm-40) REVERT: A 99 TYR cc_start: 0.8938 (p90) cc_final: 0.8711 (p90) REVERT: A 147 CYS cc_start: 0.3339 (p) cc_final: 0.3054 (p) REVERT: B 547 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7414 (tp) REVERT: B 595 GLN cc_start: 0.7434 (pt0) cc_final: 0.7013 (tp40) REVERT: B 596 ARG cc_start: 0.7974 (mtt-85) cc_final: 0.7758 (mtt-85) REVERT: E 100 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7456 (mm-30) REVERT: E 117 ASP cc_start: 0.7333 (m-30) cc_final: 0.6635 (p0) REVERT: H 32 TYR cc_start: 0.8550 (m-80) cc_final: 0.8014 (m-10) REVERT: H 96 PHE cc_start: 0.8380 (m-80) cc_final: 0.8160 (m-10) REVERT: I 251 GLU cc_start: 0.8004 (pm20) cc_final: 0.7436 (pm20) REVERT: K 37 ASP cc_start: 0.7052 (p0) cc_final: 0.6760 (p0) REVERT: K 96 GLN cc_start: 0.7958 (pp30) cc_final: 0.7699 (pp30) outliers start: 36 outliers final: 28 residues processed: 351 average time/residue: 0.2419 time to fit residues: 122.2411 Evaluate side-chains 325 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 296 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 109 TYR Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 188 GLN Chi-restraints excluded: chain D residue 573 LEU Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain F residue 544 THR Chi-restraints excluded: chain F residue 549 HIS 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 183 LEU Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 152 LEU Chi-restraints excluded: chain H residue 250 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 91 ASP Chi-restraints excluded: chain I residue 142 ASP Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain K residue 20 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 7.9990 chunk 139 optimal weight: 0.9990 chunk 30 optimal weight: 7.9990 chunk 90 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 128 optimal weight: 6.9990 chunk 71 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 40 ASN ** A 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 551 GLN ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 GLN ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 52 ASN H 168 GLN ** H 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 103 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 13134 Z= 0.391 Angle : 0.688 8.449 17835 Z= 0.345 Chirality : 0.046 0.210 1985 Planarity : 0.005 0.055 2282 Dihedral : 6.880 62.724 1985 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 4.37 % Allowed : 21.49 % Favored : 74.14 % 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: -1.10 (0.21), residues: 1616 helix: 0.42 (0.48), residues: 135 sheet: -0.82 (0.21), residues: 609 loop : -0.76 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 104 HIS 0.011 0.002 HIS I 35 PHE 0.019 0.002 PHE H 29 TYR 0.017 0.002 TYR H 54 ARG 0.004 0.001 ARG E 64 *********************** 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 348 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 288 time to evaluate : 1.456 Fit side-chains revert: symmetry clash REVERT: A 62 GLN cc_start: 0.7118 (pt0) cc_final: 0.6604 (mt0) REVERT: A 103 GLU cc_start: 0.7564 (tt0) cc_final: 0.7338 (tt0) REVERT: A 112 GLU cc_start: 0.7636 (pm20) cc_final: 0.7356 (pm20) REVERT: A 140 LYS cc_start: 0.8144 (mmmm) cc_final: 0.7352 (tptp) REVERT: B 596 ARG cc_start: 0.8028 (mtt-85) cc_final: 0.7758 (mtt-85) REVERT: C 117 ASP cc_start: 0.9112 (OUTLIER) cc_final: 0.8870 (t0) REVERT: E 100 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7590 (mm-30) REVERT: E 117 ASP cc_start: 0.7415 (m-30) cc_final: 0.6690 (p0) REVERT: E 156 GLU cc_start: 0.8066 (tt0) cc_final: 0.7855 (tt0) REVERT: K 37 ASP cc_start: 0.7249 (p0) cc_final: 0.6920 (p0) REVERT: K 96 GLN cc_start: 0.8214 (pp30) cc_final: 0.7756 (pp30) outliers start: 60 outliers final: 43 residues processed: 323 average time/residue: 0.2370 time to fit residues: 110.5965 Evaluate side-chains 319 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 275 time to evaluate : 1.470 ------------------------------------------------------------------------------- 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 547 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 109 TYR Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 144 THR 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 52 VAL Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 167 SER 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 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 77 THR Chi-restraints excluded: chain G residue 144 VAL Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain H residue 72 THR 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 80 VAL Chi-restraints excluded: chain I residue 91 ASP Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 209 SER Chi-restraints excluded: chain J residue 37 VAL 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 66 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 88 optimal weight: 0.0970 chunk 113 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 130 optimal weight: 4.9990 chunk 86 optimal weight: 0.5980 chunk 154 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 chunk 94 optimal weight: 0.6980 chunk 71 optimal weight: 8.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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** ** C 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 168 GLN ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 103 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13134 Z= 0.197 Angle : 0.638 10.533 17835 Z= 0.314 Chirality : 0.044 0.206 1985 Planarity : 0.005 0.057 2282 Dihedral : 6.220 53.901 1985 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.20 % Allowed : 23.16 % Favored : 73.63 % 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: 0.52 (0.48), residues: 135 sheet: -0.74 (0.22), residues: 572 loop : -0.63 (0.21), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 104 HIS 0.007 0.001 HIS I 35 PHE 0.018 0.002 PHE G 96 TYR 0.014 0.001 TYR B 543 ARG 0.006 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 348 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 304 time to evaluate : 1.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLN cc_start: 0.6932 (pt0) cc_final: 0.6520 (mt0) REVERT: A 99 TYR cc_start: 0.8986 (p90) cc_final: 0.8643 (p90) REVERT: A 103 GLU cc_start: 0.7447 (tt0) cc_final: 0.7137 (tt0) REVERT: A 140 LYS cc_start: 0.8084 (mmmm) cc_final: 0.7364 (tptp) REVERT: B 596 ARG cc_start: 0.7970 (mtt-85) cc_final: 0.7747 (mtt-85) REVERT: C 117 ASP cc_start: 0.9077 (OUTLIER) cc_final: 0.8837 (t0) REVERT: E 56 LYS cc_start: 0.8019 (mppt) cc_final: 0.7634 (mtmm) REVERT: E 64 ARG cc_start: 0.6055 (mtm180) cc_final: 0.5796 (mtp180) REVERT: E 100 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7470 (mm-30) REVERT: E 117 ASP cc_start: 0.7479 (m-30) cc_final: 0.6720 (p0) REVERT: E 156 GLU cc_start: 0.8014 (tt0) cc_final: 0.7805 (tt0) REVERT: G 225 GLU cc_start: 0.7496 (pm20) cc_final: 0.7250 (pm20) REVERT: H 32 TYR cc_start: 0.8560 (m-80) cc_final: 0.8046 (m-10) REVERT: K 37 ASP cc_start: 0.7133 (p0) cc_final: 0.6812 (p0) REVERT: K 96 GLN cc_start: 0.8034 (pp30) cc_final: 0.7743 (pp30) outliers start: 44 outliers final: 33 residues processed: 330 average time/residue: 0.2371 time to fit residues: 113.0856 Evaluate side-chains 323 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 289 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 109 TYR Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain D residue 573 LEU Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain F residue 544 THR Chi-restraints excluded: chain F residue 549 HIS 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 77 THR Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 152 LEU Chi-restraints excluded: chain H residue 192 LEU 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 I residue 142 ASP Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 209 SER Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 20 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 121 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 ** A 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 551 GLN ** C 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 521 GLN H 168 GLN ** H 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 103 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 13134 Z= 0.390 Angle : 0.717 10.417 17835 Z= 0.356 Chirality : 0.047 0.189 1985 Planarity : 0.005 0.056 2282 Dihedral : 6.455 49.552 1985 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.20 % Allowed : 23.60 % Favored : 73.20 % 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: -1.20 (0.21), residues: 1616 helix: 0.35 (0.47), residues: 135 sheet: -0.88 (0.21), residues: 603 loop : -0.83 (0.21), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP I 36 HIS 0.012 0.002 HIS I 35 PHE 0.030 0.002 PHE H 29 TYR 0.020 0.002 TYR C 162 ARG 0.007 0.001 ARG K 18 *********************** 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 331 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 287 time to evaluate : 1.461 Fit side-chains revert: symmetry clash REVERT: A 62 GLN cc_start: 0.7080 (pt0) cc_final: 0.6651 (mt0) REVERT: A 103 GLU cc_start: 0.7555 (tt0) cc_final: 0.7351 (tt0) REVERT: A 140 LYS cc_start: 0.8217 (mmmm) cc_final: 0.7700 (tptp) REVERT: C 117 ASP cc_start: 0.9102 (OUTLIER) cc_final: 0.8888 (t0) REVERT: E 56 LYS cc_start: 0.8170 (mppt) cc_final: 0.7761 (mtmm) REVERT: E 100 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7566 (mm-30) REVERT: E 117 ASP cc_start: 0.7511 (m-30) cc_final: 0.6730 (p0) REVERT: I 251 GLU cc_start: 0.8268 (pm20) cc_final: 0.7447 (pm20) REVERT: K 37 ASP cc_start: 0.7260 (p0) cc_final: 0.6942 (p0) outliers start: 44 outliers final: 40 residues processed: 314 average time/residue: 0.2341 time to fit residues: 106.8168 Evaluate side-chains 313 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 272 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 185 ILE 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 43 LEU Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 109 TYR Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 162 TYR Chi-restraints excluded: chain D residue 573 LEU Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 52 VAL 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 F residue 527 ILE Chi-restraints excluded: chain F residue 544 THR Chi-restraints excluded: chain F residue 549 HIS 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 77 THR Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain H residue 4 LEU 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 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 87 LEU Chi-restraints excluded: chain I residue 91 ASP Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 209 SER Chi-restraints excluded: chain J residue 37 VAL 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 0.8980 chunk 147 optimal weight: 3.9990 chunk 134 optimal weight: 6.9990 chunk 143 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 129 optimal weight: 4.9990 chunk 135 optimal weight: 5.9990 chunk 94 optimal weight: 0.6980 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 ** A 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 551 GLN ** C 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 560 GLN I 174 ASN J 103 ASN K 48 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2699 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= 0.233 Angle : 0.671 8.038 17835 Z= 0.331 Chirality : 0.045 0.202 1985 Planarity : 0.005 0.056 2282 Dihedral : 5.938 51.295 1985 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.42 % Allowed : 23.96 % 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: -1.06 (0.21), residues: 1616 helix: 0.42 (0.47), residues: 135 sheet: -0.79 (0.22), residues: 568 loop : -0.75 (0.20), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP I 36 HIS 0.008 0.001 HIS I 35 PHE 0.023 0.002 PHE G 96 TYR 0.014 0.001 TYR C 162 ARG 0.006 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 340 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 293 time to evaluate : 1.567 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 GLN cc_start: 0.7047 (pt0) cc_final: 0.6620 (mt0) REVERT: A 103 GLU cc_start: 0.7479 (tt0) cc_final: 0.7233 (tt0) REVERT: A 140 LYS cc_start: 0.8146 (mmmm) cc_final: 0.7622 (tptp) REVERT: C 117 ASP cc_start: 0.9070 (OUTLIER) cc_final: 0.8866 (t0) REVERT: E 56 LYS cc_start: 0.8109 (mppt) cc_final: 0.7732 (mtmm) REVERT: E 100 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7480 (mm-30) REVERT: E 117 ASP cc_start: 0.7503 (m-30) cc_final: 0.6691 (p0) REVERT: G 225 GLU cc_start: 0.7439 (pm20) cc_final: 0.7083 (pm20) REVERT: H 96 PHE cc_start: 0.8411 (m-80) cc_final: 0.8049 (m-10) REVERT: K 37 ASP cc_start: 0.7173 (p0) cc_final: 0.6840 (p0) outliers start: 47 outliers final: 38 residues processed: 324 average time/residue: 0.2287 time to fit residues: 107.7126 Evaluate side-chains 318 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 279 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 542 ILE Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 551 GLN Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 109 TYR Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain D residue 573 LEU Chi-restraints excluded: chain E residue 52 VAL 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 F residue 544 THR Chi-restraints excluded: chain F residue 549 HIS 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 77 THR Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 234 CYS Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain H residue 4 LEU 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 54 TYR Chi-restraints excluded: chain I residue 91 ASP Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 209 SER Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain K residue 5 THR 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 151 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 105 optimal weight: 4.9990 chunk 159 optimal weight: 0.9980 chunk 146 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 ** A 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 551 GLN ** C 188 GLN ** 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 174 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 13134 Z= 0.292 Angle : 0.698 8.804 17835 Z= 0.344 Chirality : 0.046 0.194 1985 Planarity : 0.005 0.056 2282 Dihedral : 5.825 50.189 1985 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.35 % Allowed : 23.82 % Favored : 72.83 % 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: -1.12 (0.21), residues: 1616 helix: 0.40 (0.47), residues: 135 sheet: -0.82 (0.22), residues: 569 loop : -0.80 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP I 36 HIS 0.010 0.001 HIS I 35 PHE 0.032 0.002 PHE H 29 TYR 0.016 0.002 TYR C 162 ARG 0.007 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 339 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 293 time to evaluate : 1.472 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 GLN cc_start: 0.7071 (pt0) cc_final: 0.6629 (mt0) REVERT: A 103 GLU cc_start: 0.7506 (tt0) cc_final: 0.7263 (tt0) REVERT: A 140 LYS cc_start: 0.8140 (mmmm) cc_final: 0.7604 (tptp) REVERT: E 56 LYS cc_start: 0.8160 (mppt) cc_final: 0.7771 (mtmm) REVERT: E 100 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7503 (mm-30) REVERT: E 117 ASP cc_start: 0.7521 (m-30) cc_final: 0.6697 (p0) REVERT: G 228 ASP cc_start: 0.7762 (m-30) cc_final: 0.7526 (p0) REVERT: H 235 MET cc_start: 0.7782 (tpt) cc_final: 0.7537 (tpt) REVERT: I 36 TRP cc_start: 0.8143 (m100) cc_final: 0.7905 (m100) REVERT: I 82 MET cc_start: 0.7131 (OUTLIER) cc_final: 0.6538 (mtm) REVERT: I 251 GLU cc_start: 0.8273 (pm20) cc_final: 0.7419 (pm20) REVERT: K 37 ASP cc_start: 0.7185 (p0) cc_final: 0.6840 (p0) outliers start: 46 outliers final: 41 residues processed: 323 average time/residue: 0.2325 time to fit residues: 109.1766 Evaluate side-chains 316 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 274 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 542 ILE Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain B residue 551 GLN Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 109 TYR Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 573 LEU Chi-restraints excluded: chain E residue 52 VAL 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 F residue 527 ILE Chi-restraints excluded: chain F residue 544 THR Chi-restraints excluded: chain F residue 549 HIS 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 77 THR Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 227 GLU Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 234 CYS Chi-restraints excluded: chain H residue 4 LEU 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 54 TYR Chi-restraints excluded: chain I residue 82 MET Chi-restraints excluded: chain I residue 91 ASP Chi-restraints excluded: chain I residue 142 ASP Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 209 SER Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain K residue 5 THR 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: 10.0000 chunk 38 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 127 optimal weight: 10.0000 chunk 53 optimal weight: 0.8980 chunk 130 optimal weight: 0.7980 chunk 16 optimal weight: 0.0870 chunk 23 optimal weight: 0.9990 chunk 111 optimal weight: 0.0980 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 570 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.125741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.106299 restraints weight = 27754.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.109593 restraints weight = 15291.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.111864 restraints weight = 10338.227| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13134 Z= 0.201 Angle : 0.681 9.645 17835 Z= 0.336 Chirality : 0.045 0.208 1985 Planarity : 0.005 0.057 2282 Dihedral : 5.443 52.521 1985 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.77 % Allowed : 24.47 % Favored : 72.76 % 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: 0.47 (0.47), residues: 135 sheet: -0.77 (0.22), residues: 575 loop : -0.73 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP I 36 HIS 0.007 0.001 HIS I 35 PHE 0.021 0.002 PHE G 96 TYR 0.015 0.001 TYR J 32 ARG 0.006 0.000 ARG H 99 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2893.36 seconds wall clock time: 52 minutes 22.40 seconds (3142.40 seconds total)