Starting phenix.real_space_refine on Fri Jul 3 07:34:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7swd_25471/07_2026/7swd_25471.cif Found real_map, /net/cci-nas-00/data/ceres_data/7swd_25471/07_2026/7swd_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/cci-nas-00/data/ceres_data/7swd_25471/07_2026/7swd_25471.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7swd_25471/07_2026/7swd_25471.map" model { file = "/net/cci-nas-00/data/ceres_data/7swd_25471/07_2026/7swd_25471.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7swd_25471/07_2026/7swd_25471.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7swd_25471/07_2026/7swd_25471.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7swd_25471/07_2026/7swd_25471.cif" } resolution = 3.59 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12833 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1153 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 10, 'TRANS': 140} Chain breaks: 1 Chain: "B" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 758 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "C" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1153 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 10, 'TRANS': 140} Chain breaks: 1 Chain: "D" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 758 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "E" Number of atoms: 1120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1120 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 10, 'TRANS': 136} Chain breaks: 2 Chain: "F" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 758 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "G" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1734 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 213} Chain breaks: 1 Chain: "H" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1734 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 213} Chain breaks: 1 Chain: "I" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1760 Classifications: {'peptide': 229} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 216} Chain breaks: 1 Chain: "J" Number of atoms: 916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 916 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "K" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 872 Classifications: {'peptide': 113} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 106} Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.53, per 1000 atoms: 0.20 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: 0.94 Conformation dependent library (CDL) restraints added in 515.3 milliseconds 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2954 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 33 sheets defined 12.0% alpha, 30.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 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: 1.90 Time building geometry restraints manager: 1.23 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 - 17.29: 6928 17.29 - 34.59: 606 34.59 - 51.88: 104 51.88 - 69.18: 20 69.18 - 86.47: 13 Dihedral angle restraints: 7671 sinusoidal: 3007 harmonic: 4664 Sorted by residual: dihedral pdb=" CB CYS G 22 " pdb=" SG CYS G 22 " pdb=" SG CYS G 97 " pdb=" CB CYS G 97 " ideal model delta sinusoidal sigma weight residual 93.00 161.39 -68.39 1 1.00e+01 1.00e-02 6.06e+01 dihedral pdb=" CB CYS K 23 " pdb=" SG CYS K 23 " pdb=" SG CYS K 94 " pdb=" CB CYS K 94 " ideal model delta sinusoidal sigma weight residual 93.00 156.93 -63.93 1 1.00e+01 1.00e-02 5.38e+01 dihedral pdb=" CB CYS I 164 " pdb=" SG CYS I 164 " pdb=" SG CYS I 234 " pdb=" CB CYS I 234 " ideal model delta sinusoidal sigma weight residual 93.00 130.18 -37.18 1 1.00e+01 1.00e-02 1.95e+01 ... (remaining 7668 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.132: 1962 0.132 - 0.264: 18 0.264 - 0.396: 3 0.396 - 0.528: 0 0.528 - 0.660: 2 Chirality restraints: 1985 Sorted by residual: chirality pdb=" C1 NAG L 1 " pdb=" ND2 ASN B 563 " pdb=" C2 NAG L 1 " pdb=" O5 NAG L 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.74 -0.66 2.00e-01 2.50e+01 1.09e+01 chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN D 563 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.80 -0.60 2.00e-01 2.50e+01 9.14e+00 chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN F 563 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.35e+00 ... (remaining 1982 not shown) Planarity restraints: 2285 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA G 40 " -0.073 5.00e-02 4.00e+02 1.09e-01 1.88e+01 pdb=" N PRO G 41 " 0.188 5.00e-02 4.00e+02 pdb=" CA PRO G 41 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO G 41 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU I 158 " -0.056 5.00e-02 4.00e+02 8.37e-02 1.12e+01 pdb=" N PRO I 159 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO I 159 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO I 159 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 115 " 0.050 5.00e-02 4.00e+02 7.57e-02 9.17e+00 pdb=" N PRO C 116 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO C 116 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 116 " 0.042 5.00e-02 4.00e+02 ... (remaining 2282 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 281 2.68 - 3.23: 12358 3.23 - 3.79: 19756 3.79 - 4.34: 26012 4.34 - 4.90: 44123 Nonbonded interactions: 102530 Sorted by model distance: nonbonded pdb=" O6 NAG N 1 " pdb=" O7 NAG N 2 " model vdw 2.124 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: 1.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.990 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 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 13160 Z= 0.243 Angle : 0.781 10.052 17896 Z= 0.402 Chirality : 0.053 0.660 1985 Planarity : 0.006 0.109 2282 Dihedral : 13.467 86.469 4666 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 14.75 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.027 0.002 ARG K 18 TYR 0.024 0.002 TYR A 99 PHE 0.016 0.002 PHE H 217 TRP 0.042 0.003 TRP I 36 HIS 0.016 0.002 HIS F 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.24 (13134) covalent geometry : angle 0.76552 / 0.40 (17835) SS BOND : bond 0.00514 / 0.31 ( 17) SS BOND : angle 1.66396 / 1.19 ( 34) hydrogen bonds : bond 0.15545 / 10.71 ( 406) hydrogen bonds : angle 7.60003 / 5.46 ( 1053) link_BETA1-4 : bond 0.00537 / 0.27 ( 6) link_BETA1-4 : angle 1.68684 / 1.07 ( 18) link_NAG-ASN : bond 0.00482 / 0.24 ( 3) link_NAG-ASN : angle 5.88217 / 2.93 ( 9) *********************** 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 to be fit. rotamer outliers: 0 poor density : 369 time to evaluate : 0.375 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: 0.7132 (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: 0.1055 time to fit residues: 56.1176 Evaluate side-chains 285 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 0.0270 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.0980 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 0.7980 overall best weight: 0.5040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 HIS ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.128690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.110423 restraints weight = 27335.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.113751 restraints weight = 14722.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.116001 restraints weight = 9724.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.117539 restraints weight = 7243.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.118534 restraints weight = 5844.364| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13160 Z= 0.130 Angle : 0.648 9.425 17896 Z= 0.324 Chirality : 0.046 0.234 1985 Planarity : 0.005 0.065 2282 Dihedral : 4.805 22.962 1802 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.82 % Allowed : 11.29 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.21), residues: 1616 helix: 0.38 (0.44), residues: 141 sheet: -0.55 (0.22), residues: 557 loop : -0.58 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 223 TYR 0.017 0.001 TYR I 81 PHE 0.030 0.002 PHE G 96 TRP 0.027 0.002 TRP I 36 HIS 0.008 0.001 HIS I 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (13134) covalent geometry : angle 0.64303 / 0.32 (17835) SS BOND : bond 0.00456 / 0.28 ( 17) SS BOND : angle 1.42243 / 1.01 ( 34) hydrogen bonds : bond 0.04065 / 2.85 ( 406) hydrogen bonds : angle 6.13761 / 4.36 ( 1053) link_BETA1-4 : bond 0.00386 / 0.18 ( 6) link_BETA1-4 : angle 1.70104 / 1.14 ( 18) link_NAG-ASN : bond 0.00551 / 0.24 ( 3) link_NAG-ASN : angle 1.80948 / 0.96 ( 9) *********************** 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 383 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 358 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 GLN cc_start: 0.7364 (pt0) cc_final: 0.6513 (mm-40) REVERT: A 112 GLU cc_start: 0.7556 (pt0) cc_final: 0.7277 (pt0) REVERT: E 117 ASP cc_start: 0.7264 (m-30) cc_final: 0.6669 (p0) REVERT: G 74 ASP cc_start: 0.6872 (m-30) cc_final: 0.6647 (m-30) REVERT: G 249 LYS cc_start: 0.6525 (tmtt) cc_final: 0.6254 (tmmt) REVERT: I 227 GLU cc_start: 0.7506 (pm20) cc_final: 0.7045 (pp20) REVERT: J 46 GLU cc_start: 0.7360 (pt0) cc_final: 0.6625 (pt0) REVERT: K 42 TYR cc_start: 0.9002 (m-80) cc_final: 0.8699 (m-10) REVERT: K 96 GLN cc_start: 0.8011 (pp30) cc_final: 0.7784 (pp30) outliers start: 25 outliers final: 19 residues processed: 365 average time/residue: 0.0998 time to fit residues: 53.0119 Evaluate side-chains 311 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 292 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 J residue 37 VAL Chi-restraints excluded: chain J residue 104 TRP Chi-restraints excluded: chain J residue 116 GLN Chi-restraints excluded: chain K residue 20 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 157 optimal weight: 0.7980 chunk 107 optimal weight: 8.9990 chunk 134 optimal weight: 9.9990 chunk 109 optimal weight: 0.9980 chunk 66 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 chunk 4 optimal weight: 0.0050 chunk 104 optimal weight: 0.3980 chunk 8 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 overall best weight: 1.0396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS B 521 GLN ** C 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 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** I 239 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.127363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.108152 restraints weight = 27814.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.111453 restraints weight = 15377.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.113723 restraints weight = 10357.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.115238 restraints weight = 7819.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.116251 restraints weight = 6411.923| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13160 Z= 0.138 Angle : 0.615 11.334 17896 Z= 0.307 Chirality : 0.044 0.171 1985 Planarity : 0.005 0.059 2282 Dihedral : 4.685 23.027 1802 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.48 % Allowed : 15.29 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.21), residues: 1616 helix: 0.57 (0.46), residues: 141 sheet: -0.58 (0.22), residues: 562 loop : -0.54 (0.20), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 164 TYR 0.016 0.001 TYR B 543 PHE 0.018 0.001 PHE B 592 TRP 0.036 0.002 TRP B 531 HIS 0.009 0.001 HIS I 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (13134) covalent geometry : angle 0.61005 / 0.31 (17835) SS BOND : bond 0.00443 / 0.26 ( 17) SS BOND : angle 1.43568 / 0.97 ( 34) hydrogen bonds : bond 0.03716 / 2.57 ( 406) hydrogen bonds : angle 5.83394 / 4.14 ( 1053) link_BETA1-4 : bond 0.00482 / 0.22 ( 6) link_BETA1-4 : angle 1.56418 / 0.97 ( 18) link_NAG-ASN : bond 0.00275 / 0.11 ( 3) link_NAG-ASN : angle 1.40076 / 0.75 ( 9) *********************** 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 352 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 318 time to evaluate : 0.501 Fit side-chains revert: symmetry clash REVERT: A 62 GLN cc_start: 0.6990 (pt0) cc_final: 0.6419 (mm-40) REVERT: E 100 GLU cc_start: 0.8250 (mm-30) cc_final: 0.7810 (mm-30) REVERT: E 117 ASP cc_start: 0.7158 (m-30) cc_final: 0.6589 (p0) REVERT: G 32 TYR cc_start: 0.8394 (m-80) cc_final: 0.8182 (m-80) REVERT: G 74 ASP cc_start: 0.6965 (m-30) cc_final: 0.6754 (m-30) REVERT: G 249 LYS cc_start: 0.6509 (tmtt) cc_final: 0.6265 (tmmt) REVERT: I 251 GLU cc_start: 0.8081 (pm20) cc_final: 0.7446 (pm20) REVERT: J 77 THR cc_start: 0.8003 (p) cc_final: 0.7601 (t) REVERT: K 42 TYR cc_start: 0.9040 (m-80) cc_final: 0.8759 (m-10) REVERT: K 96 GLN cc_start: 0.8078 (pp30) cc_final: 0.7780 (pp30) outliers start: 34 outliers final: 31 residues processed: 332 average time/residue: 0.1004 time to fit residues: 49.2314 Evaluate side-chains 328 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 297 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 CYS Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 147 CYS Chi-restraints excluded: chain D residue 545 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 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 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 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 9 ASP Chi-restraints excluded: chain K residue 20 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 148 optimal weight: 6.9990 chunk 149 optimal weight: 0.0170 chunk 143 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 153 optimal weight: 0.4980 chunk 130 optimal weight: 5.9990 chunk 125 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 136 optimal weight: 0.9990 overall best weight: 1.5024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS C 188 GLN ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 GLN K 48 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.125914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.106687 restraints weight = 27936.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.109943 restraints weight = 15515.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.112186 restraints weight = 10478.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.113651 restraints weight = 7933.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.114630 restraints weight = 6536.561| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13160 Z= 0.162 Angle : 0.620 8.109 17896 Z= 0.311 Chirality : 0.044 0.182 1985 Planarity : 0.005 0.058 2282 Dihedral : 4.688 23.492 1802 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.57 % Allowed : 17.70 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.21), residues: 1616 helix: 0.62 (0.46), residues: 141 sheet: -0.62 (0.22), residues: 569 loop : -0.60 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 18 TYR 0.013 0.001 TYR B 543 PHE 0.018 0.002 PHE G 96 TRP 0.037 0.002 TRP E 104 HIS 0.010 0.001 HIS I 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 (13134) covalent geometry : angle 0.61254 / 0.31 (17835) SS BOND : bond 0.00452 / 0.26 ( 17) SS BOND : angle 2.02791 / 1.21 ( 34) hydrogen bonds : bond 0.03659 / 2.54 ( 406) hydrogen bonds : angle 5.75254 / 4.08 ( 1053) link_BETA1-4 : bond 0.00440 / 0.20 ( 6) link_BETA1-4 : angle 1.52448 / 0.93 ( 18) link_NAG-ASN : bond 0.00252 / 0.11 ( 3) link_NAG-ASN : angle 1.26657 / 0.67 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 314 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 GLN cc_start: 0.6987 (pt0) cc_final: 0.6512 (mm-40) REVERT: B 531 TRP cc_start: 0.8321 (p-90) cc_final: 0.8104 (p-90) REVERT: E 100 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7833 (mm-30) REVERT: E 117 ASP cc_start: 0.7198 (m-30) cc_final: 0.6628 (p0) REVERT: G 32 TYR cc_start: 0.8326 (m-80) cc_final: 0.8118 (m-80) REVERT: G 36 TRP cc_start: 0.8157 (m100) cc_final: 0.7579 (m100) REVERT: G 249 LYS cc_start: 0.6567 (tmtt) cc_final: 0.6320 (tmmt) REVERT: H 82 MET cc_start: 0.7506 (ttt) cc_final: 0.7266 (ttt) REVERT: I 251 GLU cc_start: 0.8130 (pm20) cc_final: 0.7504 (pm20) REVERT: K 37 ASP cc_start: 0.7055 (p0) cc_final: 0.6828 (p0) REVERT: K 42 TYR cc_start: 0.9002 (m-80) cc_final: 0.8324 (m-10) REVERT: K 96 GLN cc_start: 0.8120 (pp30) cc_final: 0.7798 (pp30) outliers start: 49 outliers final: 39 residues processed: 342 average time/residue: 0.1075 time to fit residues: 54.2016 Evaluate side-chains 334 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 295 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 108 CYS Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 132 PHE Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 147 CYS Chi-restraints excluded: chain C residue 188 GLN Chi-restraints excluded: chain D residue 592 PHE Chi-restraints excluded: chain E residue 52 VAL 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 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 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 153 optimal weight: 0.2980 chunk 106 optimal weight: 0.1980 chunk 127 optimal weight: 9.9990 chunk 111 optimal weight: 9.9990 chunk 47 optimal weight: 8.9990 chunk 10 optimal weight: 9.9990 chunk 80 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 124 optimal weight: 9.9990 chunk 145 optimal weight: 9.9990 chunk 141 optimal weight: 7.9990 overall best weight: 2.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS C 62 GLN 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 ** H 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 239 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.122951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.104091 restraints weight = 27932.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.107225 restraints weight = 15407.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.109403 restraints weight = 10441.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.110899 restraints weight = 7927.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.111672 restraints weight = 6480.714| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 13160 Z= 0.224 Angle : 0.667 8.960 17896 Z= 0.334 Chirality : 0.045 0.194 1985 Planarity : 0.005 0.056 2282 Dihedral : 4.859 24.473 1802 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.86 % Allowed : 19.45 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.21), residues: 1616 helix: 0.53 (0.47), residues: 135 sheet: -0.76 (0.22), residues: 580 loop : -0.66 (0.20), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 18 TYR 0.014 0.002 TYR H 232 PHE 0.017 0.002 PHE G 96 TRP 0.023 0.002 TRP E 104 HIS 0.010 0.001 HIS I 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.22 (13134) covalent geometry : angle 0.66066 / 0.33 (17835) SS BOND : bond 0.01036 / 0.77 ( 17) SS BOND : angle 1.88956 / 1.14 ( 34) hydrogen bonds : bond 0.03798 / 2.62 ( 406) hydrogen bonds : angle 5.83888 / 4.15 ( 1053) link_BETA1-4 : bond 0.00452 / 0.21 ( 6) link_BETA1-4 : angle 1.49141 / 0.90 ( 18) link_NAG-ASN : bond 0.00246 / 0.13 ( 3) link_NAG-ASN : angle 1.41980 / 0.75 ( 9) *********************** 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 354 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 301 time to evaluate : 0.504 Fit side-chains REVERT: A 62 GLN cc_start: 0.6957 (pt0) cc_final: 0.6546 (mm-40) REVERT: B 595 GLN cc_start: 0.7456 (pt0) cc_final: 0.7086 (tp-100) REVERT: C 117 ASP cc_start: 0.9182 (OUTLIER) cc_final: 0.8935 (t0) REVERT: E 64 ARG cc_start: 0.5955 (ttp-170) cc_final: 0.5737 (mtm180) REVERT: E 100 GLU cc_start: 0.8263 (mm-30) cc_final: 0.7866 (mm-30) REVERT: E 117 ASP cc_start: 0.7275 (m-30) cc_final: 0.6642 (p0) REVERT: G 36 TRP cc_start: 0.8319 (m100) cc_final: 0.7576 (m100) REVERT: G 249 LYS cc_start: 0.6645 (tmtt) cc_final: 0.6404 (tmmt) REVERT: H 82 MET cc_start: 0.7492 (ttt) cc_final: 0.7254 (ttt) REVERT: H 96 PHE cc_start: 0.8642 (m-80) cc_final: 0.8375 (m-80) REVERT: K 37 ASP cc_start: 0.7229 (p0) cc_final: 0.6908 (p0) REVERT: K 42 TYR cc_start: 0.9036 (m-80) cc_final: 0.8503 (m-10) REVERT: K 96 GLN cc_start: 0.8251 (pp30) cc_final: 0.7849 (pp30) outliers start: 53 outliers final: 42 residues processed: 331 average time/residue: 0.1080 time to fit residues: 52.7262 Evaluate side-chains 321 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 278 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 108 CYS Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 132 PHE Chi-restraints excluded: chain C residue 144 THR 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 174 ASN Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 227 GLU Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain H residue 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 156 optimal weight: 5.9990 chunk 126 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 2 optimal weight: 9.9990 chunk 91 optimal weight: 7.9990 chunk 14 optimal weight: 0.9980 chunk 144 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS C 62 GLN 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** ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 174 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.125132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.106421 restraints weight = 27521.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.109591 restraints weight = 15195.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.111803 restraints weight = 10253.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.113282 restraints weight = 7743.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.114233 restraints weight = 6329.560| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13160 Z= 0.141 Angle : 0.630 8.457 17896 Z= 0.313 Chirality : 0.044 0.170 1985 Planarity : 0.005 0.057 2282 Dihedral : 4.712 24.463 1802 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.71 % Allowed : 20.25 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.21), residues: 1616 helix: 0.59 (0.48), residues: 135 sheet: -0.75 (0.22), residues: 579 loop : -0.60 (0.21), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 67 TYR 0.014 0.001 TYR C 162 PHE 0.016 0.001 PHE G 96 TRP 0.018 0.001 TRP E 104 HIS 0.009 0.001 HIS F 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (13134) covalent geometry : angle 0.62441 / 0.31 (17835) SS BOND : bond 0.00393 / 0.22 ( 17) SS BOND : angle 1.76094 / 1.06 ( 34) hydrogen bonds : bond 0.03533 / 2.44 ( 406) hydrogen bonds : angle 5.64904 / 3.98 ( 1053) link_BETA1-4 : bond 0.00402 / 0.19 ( 6) link_BETA1-4 : angle 1.47000 / 0.92 ( 18) link_NAG-ASN : bond 0.00210 / 0.09 ( 3) link_NAG-ASN : angle 1.30724 / 0.69 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 304 time to evaluate : 0.439 Fit side-chains REVERT: A 62 GLN cc_start: 0.6978 (pt0) cc_final: 0.6593 (mm-40) REVERT: B 595 GLN cc_start: 0.7333 (pt0) cc_final: 0.6962 (tp-100) REVERT: C 117 ASP cc_start: 0.9171 (OUTLIER) cc_final: 0.8970 (t0) REVERT: E 100 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7755 (mm-30) REVERT: E 117 ASP cc_start: 0.7382 (m-30) cc_final: 0.6678 (p0) REVERT: G 18 VAL cc_start: 0.7931 (t) cc_final: 0.7643 (m) REVERT: G 36 TRP cc_start: 0.8271 (m100) cc_final: 0.7590 (m100) REVERT: G 249 LYS cc_start: 0.6602 (tmtt) cc_final: 0.6401 (tmmt) REVERT: H 82 MET cc_start: 0.7440 (ttt) cc_final: 0.7230 (ttt) REVERT: K 37 ASP cc_start: 0.7255 (p0) cc_final: 0.6920 (p0) REVERT: K 42 TYR cc_start: 0.8983 (m-80) cc_final: 0.8470 (m-10) REVERT: K 96 GLN cc_start: 0.8157 (pp30) cc_final: 0.7804 (pp30) outliers start: 51 outliers final: 40 residues processed: 333 average time/residue: 0.1057 time to fit residues: 51.9490 Evaluate side-chains 322 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 281 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain B residue 506 ASN Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 132 PHE Chi-restraints excluded: chain C residue 147 CYS Chi-restraints excluded: chain C residue 188 GLN Chi-restraints excluded: chain D residue 545 GLU 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 225 GLU 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 192 LEU Chi-restraints excluded: chain H residue 239 GLN Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 54 TYR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 80 VAL 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 31 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 152 optimal weight: 5.9990 chunk 142 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 143 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 111 optimal weight: 8.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS ** 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 52 ASN ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 174 ASN K 48 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.124461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.105477 restraints weight = 27619.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.108650 restraints weight = 15335.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.110845 restraints weight = 10409.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.112350 restraints weight = 7909.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.113285 restraints weight = 6470.922| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13160 Z= 0.153 Angle : 0.631 8.104 17896 Z= 0.315 Chirality : 0.044 0.180 1985 Planarity : 0.005 0.056 2282 Dihedral : 4.694 24.376 1802 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.86 % Allowed : 21.70 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.21), residues: 1616 helix: 0.44 (0.48), residues: 135 sheet: -0.75 (0.22), residues: 567 loop : -0.62 (0.20), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 18 TYR 0.018 0.001 TYR H 54 PHE 0.024 0.002 PHE G 96 TRP 0.016 0.001 TRP I 36 HIS 0.007 0.001 HIS I 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 (13134) covalent geometry : angle 0.62584 / 0.31 (17835) SS BOND : bond 0.00381 / 0.21 ( 17) SS BOND : angle 1.62739 / 1.01 ( 34) hydrogen bonds : bond 0.03495 / 2.40 ( 406) hydrogen bonds : angle 5.59724 / 3.93 ( 1053) link_BETA1-4 : bond 0.00430 / 0.20 ( 6) link_BETA1-4 : angle 1.45880 / 0.91 ( 18) link_NAG-ASN : bond 0.00256 / 0.11 ( 3) link_NAG-ASN : angle 1.35483 / 0.71 ( 9) *********************** 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 344 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 291 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 GLN cc_start: 0.6936 (pt0) cc_final: 0.6429 (mt0) REVERT: E 100 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7710 (mm-30) REVERT: E 117 ASP cc_start: 0.7411 (m-30) cc_final: 0.6675 (p0) REVERT: G 18 VAL cc_start: 0.7835 (t) cc_final: 0.7585 (m) REVERT: G 36 TRP cc_start: 0.8280 (m100) cc_final: 0.7580 (m100) REVERT: H 32 TYR cc_start: 0.8676 (m-80) cc_final: 0.8118 (m-10) REVERT: H 82 MET cc_start: 0.7441 (ttt) cc_final: 0.7219 (ttt) REVERT: H 96 PHE cc_start: 0.8557 (m-80) cc_final: 0.8234 (m-10) REVERT: K 37 ASP cc_start: 0.7236 (p0) cc_final: 0.6885 (p0) REVERT: K 42 TYR cc_start: 0.8951 (m-80) cc_final: 0.8484 (m-10) REVERT: K 96 GLN cc_start: 0.8169 (pp30) cc_final: 0.7792 (pp30) outliers start: 53 outliers final: 44 residues processed: 321 average time/residue: 0.1091 time to fit residues: 51.4492 Evaluate side-chains 323 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 279 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain B residue 506 ASN Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 132 PHE Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 147 CYS Chi-restraints excluded: chain D residue 545 GLU 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 227 GLU Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 37 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 192 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 91 ASP Chi-restraints excluded: chain I residue 142 ASP Chi-restraints excluded: chain I residue 209 SER Chi-restraints excluded: chain J residue 30 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 Chi-restraints excluded: chain K residue 66 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 37 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 159 optimal weight: 1.9990 chunk 154 optimal weight: 3.9990 chunk 88 optimal weight: 0.3980 chunk 150 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 chunk 64 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS B 551 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 ** H 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.122988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.103978 restraints weight = 27686.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.107100 restraints weight = 15473.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.109256 restraints weight = 10502.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.110631 restraints weight = 7997.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.111696 restraints weight = 6627.160| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 13160 Z= 0.194 Angle : 0.661 12.623 17896 Z= 0.329 Chirality : 0.045 0.177 1985 Planarity : 0.005 0.057 2282 Dihedral : 4.795 24.380 1802 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 4.01 % Allowed : 22.07 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.21), residues: 1616 helix: 0.48 (0.48), residues: 135 sheet: -0.83 (0.21), residues: 600 loop : -0.71 (0.21), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 18 TYR 0.018 0.002 TYR C 162 PHE 0.020 0.002 PHE G 96 TRP 0.016 0.002 TRP I 36 HIS 0.008 0.001 HIS I 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.19 (13134) covalent geometry : angle 0.65488 / 0.33 (17835) SS BOND : bond 0.00453 / 0.26 ( 17) SS BOND : angle 1.78297 / 1.02 ( 34) hydrogen bonds : bond 0.03637 / 2.51 ( 406) hydrogen bonds : angle 5.64811 / 3.99 ( 1053) link_BETA1-4 : bond 0.00392 / 0.19 ( 6) link_BETA1-4 : angle 1.43394 / 0.89 ( 18) link_NAG-ASN : bond 0.00275 / 0.14 ( 3) link_NAG-ASN : angle 1.41181 / 0.71 ( 9) *********************** 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 346 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 291 time to evaluate : 0.496 Fit side-chains REVERT: A 62 GLN cc_start: 0.6976 (pt0) cc_final: 0.6488 (mt0) REVERT: E 100 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7742 (mm-30) REVERT: E 117 ASP cc_start: 0.7440 (m-30) cc_final: 0.6687 (p0) REVERT: E 156 GLU cc_start: 0.8187 (tt0) cc_final: 0.7938 (tt0) REVERT: G 36 TRP cc_start: 0.8346 (m100) cc_final: 0.7698 (m100) REVERT: H 32 TYR cc_start: 0.8709 (m-80) cc_final: 0.8144 (m-10) REVERT: H 82 MET cc_start: 0.7404 (ttt) cc_final: 0.7189 (ttt) REVERT: H 96 PHE cc_start: 0.8527 (m-80) cc_final: 0.8147 (m-10) REVERT: H 168 GLN cc_start: 0.8238 (tm130) cc_final: 0.7996 (tm-30) REVERT: I 36 TRP cc_start: 0.8336 (m100) cc_final: 0.8103 (m100) REVERT: K 37 ASP cc_start: 0.7301 (p0) cc_final: 0.6926 (p0) REVERT: K 42 TYR cc_start: 0.9010 (m-80) cc_final: 0.8494 (m-10) REVERT: K 48 GLN cc_start: 0.8055 (tp-100) cc_final: 0.7742 (tp40) REVERT: K 96 GLN cc_start: 0.8230 (pp30) cc_final: 0.7827 (pp30) outliers start: 55 outliers final: 47 residues processed: 323 average time/residue: 0.1083 time to fit residues: 51.4124 Evaluate side-chains 323 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 276 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain B residue 506 ASN Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 551 GLN Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 132 PHE Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain 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 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 250 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 52 ASN Chi-restraints excluded: chain H residue 72 THR 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 72 THR Chi-restraints excluded: chain I residue 80 VAL 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 30 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 19 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 154 optimal weight: 4.9990 chunk 79 optimal weight: 7.9990 chunk 40 optimal weight: 0.6980 chunk 153 optimal weight: 0.0370 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS A 40 ASN D 508 GLN D 560 GLN ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 103 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.125635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.106505 restraints weight = 27692.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.109710 restraints weight = 15398.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.111905 restraints weight = 10453.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.113384 restraints weight = 7956.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.114358 restraints weight = 6543.341| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13160 Z= 0.120 Angle : 0.647 12.735 17896 Z= 0.318 Chirality : 0.044 0.185 1985 Planarity : 0.005 0.059 2282 Dihedral : 4.633 24.129 1802 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.06 % Allowed : 22.94 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.21), residues: 1616 helix: 0.58 (0.48), residues: 135 sheet: -0.79 (0.22), residues: 570 loop : -0.63 (0.20), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 18 TYR 0.014 0.001 TYR H 54 PHE 0.021 0.001 PHE G 96 TRP 0.015 0.001 TRP E 104 HIS 0.006 0.001 HIS I 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (13134) covalent geometry : angle 0.64282 / 0.32 (17835) SS BOND : bond 0.00397 / 0.24 ( 17) SS BOND : angle 1.47295 / 0.88 ( 34) hydrogen bonds : bond 0.03341 / 2.28 ( 406) hydrogen bonds : angle 5.45719 / 3.83 ( 1053) link_BETA1-4 : bond 0.00406 / 0.20 ( 6) link_BETA1-4 : angle 1.45464 / 0.93 ( 18) link_NAG-ASN : bond 0.00197 / 0.08 ( 3) link_NAG-ASN : angle 1.29571 / 0.69 ( 9) *********************** 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 337 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 295 time to evaluate : 0.473 Fit side-chains REVERT: A 62 GLN cc_start: 0.6921 (pt0) cc_final: 0.6533 (mt0) REVERT: E 100 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7731 (mm-30) REVERT: E 117 ASP cc_start: 0.7503 (m-30) cc_final: 0.6734 (p0) REVERT: E 156 GLU cc_start: 0.8129 (tt0) cc_final: 0.7840 (tt0) REVERT: G 36 TRP cc_start: 0.8250 (m100) cc_final: 0.7655 (m100) REVERT: H 32 TYR cc_start: 0.8659 (m-80) cc_final: 0.8156 (m-10) REVERT: H 82 MET cc_start: 0.7308 (ttt) cc_final: 0.7090 (ttt) REVERT: H 168 GLN cc_start: 0.8223 (tm130) cc_final: 0.7973 (tm-30) REVERT: I 36 TRP cc_start: 0.8207 (m100) cc_final: 0.7957 (m100) REVERT: K 37 ASP cc_start: 0.7198 (p0) cc_final: 0.6866 (p0) REVERT: K 96 GLN cc_start: 0.8160 (pp30) cc_final: 0.7778 (pp30) outliers start: 42 outliers final: 39 residues processed: 318 average time/residue: 0.1109 time to fit residues: 51.9416 Evaluate side-chains 320 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 281 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain B residue 506 ASN Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 551 GLN Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 132 PHE Chi-restraints excluded: chain D residue 573 LEU Chi-restraints excluded: chain E residue 52 VAL 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 227 GLU 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 192 LEU Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 54 TYR Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 142 ASP Chi-restraints excluded: chain I residue 209 SER Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 30 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 26 optimal weight: 4.9990 chunk 24 optimal weight: 8.9990 chunk 134 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 148 optimal weight: 0.7980 chunk 119 optimal weight: 8.9990 chunk 159 optimal weight: 0.4980 chunk 83 optimal weight: 5.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS A 40 ASN ** A 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 551 GLN ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 521 GLN ** H 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 103 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.122269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.103271 restraints weight = 28184.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.106406 restraints weight = 15584.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.108543 restraints weight = 10569.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.110005 restraints weight = 8060.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.110925 restraints weight = 6641.844| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 13160 Z= 0.229 Angle : 0.697 11.693 17896 Z= 0.348 Chirality : 0.046 0.179 1985 Planarity : 0.005 0.057 2282 Dihedral : 4.895 24.360 1802 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 3.28 % Allowed : 22.43 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.21), residues: 1616 helix: 0.45 (0.48), residues: 135 sheet: -0.85 (0.21), residues: 594 loop : -0.76 (0.20), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 134 TYR 0.020 0.002 TYR C 162 PHE 0.028 0.002 PHE H 29 TRP 0.061 0.002 TRP E 104 HIS 0.011 0.001 HIS I 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.23 (13134) covalent geometry : angle 0.69166 / 0.35 (17835) SS BOND : bond 0.00499 / 0.27 ( 17) SS BOND : angle 1.65858 / 0.96 ( 34) hydrogen bonds : bond 0.03742 / 2.59 ( 406) hydrogen bonds : angle 5.69602 / 4.02 ( 1053) link_BETA1-4 : bond 0.00488 / 0.22 ( 6) link_BETA1-4 : angle 1.44858 / 0.89 ( 18) link_NAG-ASN : bond 0.00322 / 0.17 ( 3) link_NAG-ASN : angle 1.55966 / 0.77 ( 9) ********************** 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 323 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 278 time to evaluate : 0.526 Fit side-chains REVERT: A 62 GLN cc_start: 0.7018 (pt0) cc_final: 0.6558 (mt0) REVERT: E 100 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7765 (mm-30) REVERT: E 117 ASP cc_start: 0.7552 (m-30) cc_final: 0.6765 (p0) REVERT: G 36 TRP cc_start: 0.8345 (m100) cc_final: 0.7675 (m100) REVERT: H 82 MET cc_start: 0.7448 (ttt) cc_final: 0.7241 (ttt) REVERT: H 168 GLN cc_start: 0.8223 (tm130) cc_final: 0.7916 (tm-30) REVERT: I 36 TRP cc_start: 0.8340 (m100) cc_final: 0.8030 (m100) REVERT: K 37 ASP cc_start: 0.7386 (p0) cc_final: 0.7036 (p0) REVERT: K 96 GLN cc_start: 0.8302 (pp30) cc_final: 0.7865 (pp30) outliers start: 45 outliers final: 41 residues processed: 307 average time/residue: 0.1109 time to fit residues: 50.0180 Evaluate side-chains 302 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 261 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain B residue 506 ASN Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 551 GLN Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 132 PHE Chi-restraints excluded: chain D residue 573 LEU Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 56 LYS 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 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 192 LEU Chi-restraints excluded: chain I residue 18 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 59 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 123 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 144 optimal weight: 0.8980 chunk 117 optimal weight: 7.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS A 40 ASN ** A 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 551 GLN ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 236 GLN I 6 GLN ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 174 ASN J 103 ASN ** K 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.124175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.104752 restraints weight = 27927.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.107988 restraints weight = 15448.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.110207 restraints weight = 10449.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.111598 restraints weight = 7949.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.112718 restraints weight = 6610.749| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13160 Z= 0.147 Angle : 0.672 12.010 17896 Z= 0.333 Chirality : 0.045 0.173 1985 Planarity : 0.005 0.090 2282 Dihedral : 4.801 24.225 1802 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.64 % Allowed : 22.58 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.21), residues: 1616 helix: -0.23 (0.45), residues: 153 sheet: -0.83 (0.22), residues: 570 loop : -0.70 (0.21), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 87 TYR 0.014 0.001 TYR C 162 PHE 0.020 0.002 PHE H 96 TRP 0.049 0.002 TRP E 104 HIS 0.011 0.001 HIS I 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (13134) covalent geometry : angle 0.66710 / 0.33 (17835) SS BOND : bond 0.00526 / 0.36 ( 17) SS BOND : angle 1.63056 / 1.00 ( 34) hydrogen bonds : bond 0.03530 / 2.46 ( 406) hydrogen bonds : angle 5.58870 / 3.92 ( 1053) link_BETA1-4 : bond 0.00389 / 0.19 ( 6) link_BETA1-4 : angle 1.41218 / 0.89 ( 18) link_NAG-ASN : bond 0.00190 / 0.08 ( 3) link_NAG-ASN : angle 1.43943 / 0.74 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2279.37 seconds wall clock time: 40 minutes 15.88 seconds (2415.88 seconds total)