Starting phenix.real_space_refine on Thu Aug 6 18:55:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oss_70809/08_2026/9oss_70809.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oss_70809/08_2026/9oss_70809.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9oss_70809/08_2026/9oss_70809.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oss_70809/08_2026/9oss_70809.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9oss_70809/08_2026/9oss_70809.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oss_70809/08_2026/9oss_70809.map" } resolution = 2.76 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= 0.001 sd= 0.020 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 74 5.16 5 C 10313 2.51 5 N 2849 2.21 5 O 3146 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16382 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2407 Classifications: {'peptide': 321} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 20, 'TRANS': 300} Chain breaks: 1 Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 11, 'ASN:plan1': 3, 'ARG:plan': 1, 'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 83 Chain: "B" Number of atoms: 1334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1334 Classifications: {'peptide': 169} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 1, 'TRANS': 167} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 2386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2386 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 20, 'TRANS': 298} Chain breaks: 1 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 12, 'ASN:plan1': 3, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 84 Chain: "D" Number of atoms: 1312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1312 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 1, 'TRANS': 165} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "E" Number of atoms: 2400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2400 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 20, 'TRANS': 299} Chain breaks: 1 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 10, 'ASN:plan1': 3, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 76 Chain: "F" Number of atoms: 1332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1332 Classifications: {'peptide': 169} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 1, 'TRANS': 167} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 25 Chain: "H" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 958 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 120} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 785 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 10 Chain: "J" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 950 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 120} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 780 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 15 Chain: "M" Number of atoms: 954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 954 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 120} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 784 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Time building chain proxies: 3.58, per 1000 atoms: 0.22 Number of scatterers: 16382 At special positions: 0 Unit cell: (111.09, 124.844, 147.062, 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 74 16.00 O 3146 8.00 N 2849 7.00 C 10313 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS B 137 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS D 137 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.03 Simple disulfide: pdb=" SG CYS E 14 " - pdb=" SG CYS F 137 " distance=2.03 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 76 " distance=2.03 Simple disulfide: pdb=" SG CYS E 97 " - pdb=" SG CYS E 139 " distance=2.03 Simple disulfide: pdb=" SG CYS E 281 " - pdb=" SG CYS E 305 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 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 Time building additional restraints: 1.04 Conformation dependent library (CDL) restraints added in 741.0 milliseconds 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3944 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 50 sheets defined 20.9% alpha, 29.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 73 through 80 removed outlier: 3.920A pdb=" N GLU A 77 " --> pdb=" O PRO A 74 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU A 78 " --> pdb=" O GLU A 75 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE A 80 " --> pdb=" O GLU A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 114 Processing helix chain 'A' and resid 125 through 127 removed outlier: 4.312A pdb=" N TRP A 127 " --> pdb=" O LYS A 125A" (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 196 removed outlier: 3.581A pdb=" N ALA A 193 " --> pdb=" O GLY A 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 58 removed outlier: 3.612A pdb=" N LYS B 58 " --> pdb=" O SER B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 126 removed outlier: 3.581A pdb=" N GLU B 78 " --> pdb=" O GLU B 74 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU B 105 " --> pdb=" O LEU B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 155 Processing helix chain 'B' and resid 158 through 170 removed outlier: 3.849A pdb=" N TYR B 162 " --> pdb=" O ASP B 158 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N GLU B 164 " --> pdb=" O PRO B 160 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N GLU B 165 " --> pdb=" O LYS B 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 71 Processing helix chain 'C' and resid 73 through 80 removed outlier: 3.991A pdb=" N GLU C 77 " --> pdb=" O PRO C 74 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N LEU C 78 " --> pdb=" O GLU C 75 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE C 80 " --> pdb=" O GLU C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 114 removed outlier: 3.521A pdb=" N SER C 114 " --> pdb=" O GLU C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 125A through 127 removed outlier: 4.014A pdb=" N SER C 126 " --> pdb=" O LYS C 125A" (cutoff:3.500A) removed outlier: 4.467A pdb=" N TRP C 127 " --> pdb=" O GLU C 125B" (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 125A through 127' Processing helix chain 'C' and resid 187 through 192 removed outlier: 4.089A pdb=" N ARG C 192 " --> pdb=" O ILE C 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 58 Processing helix chain 'D' and resid 74 through 126 Processing helix chain 'D' and resid 145 through 155 Processing helix chain 'D' and resid 159 through 161 No H-bonds generated for 'chain 'D' and resid 159 through 161' Processing helix chain 'D' and resid 162 through 170 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 73 through 80 removed outlier: 3.824A pdb=" N GLU E 77 " --> pdb=" O PRO E 74 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N LEU E 78 " --> pdb=" O GLU E 75 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE E 80 " --> pdb=" O GLU E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 114 Processing helix chain 'E' and resid 187 through 192 removed outlier: 3.572A pdb=" N GLN E 191 " --> pdb=" O ASN E 187 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ARG E 192 " --> pdb=" O ILE E 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 187 through 192' Processing helix chain 'F' and resid 37 through 58 removed outlier: 3.726A pdb=" N LYS F 58 " --> pdb=" O SER F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 126 removed outlier: 3.619A pdb=" N GLU F 105 " --> pdb=" O LEU F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 155 Processing helix chain 'F' and resid 158 through 170 removed outlier: 3.684A pdb=" N TYR F 162 " --> pdb=" O ASP F 158 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N GLU F 164 " --> pdb=" O PRO F 160 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N GLU F 165 " --> pdb=" O LYS F 161 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.960A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 26 through 28 Processing helix chain 'I' and resid 79 through 83 removed outlier: 4.052A pdb=" N GLU I 83 " --> pdb=" O ALA I 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 30 No H-bonds generated for 'chain 'J' and resid 28 through 30' Processing helix chain 'J' and resid 83 through 87 removed outlier: 4.068A pdb=" N THR J 87 " --> pdb=" O ALA J 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.994A pdb=" N GLU K 83 " --> pdb=" O ALA K 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 30 No H-bonds generated for 'chain 'M' and resid 28 through 30' Processing helix chain 'M' and resid 83 through 87 removed outlier: 3.919A pdb=" N THR M 87 " --> pdb=" O ALA M 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 removed outlier: 4.066A pdb=" N GLU N 83 " --> pdb=" O ALA N 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 31 through 36 removed outlier: 6.597A pdb=" N CYS B 137 " --> pdb=" O ILE B 133 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 53 removed outlier: 6.048A pdb=" N LEU A 51 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N CYS A 277 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 59 through 60 removed outlier: 6.482A pdb=" N LEU A 59 " --> pdb=" O VAL A 88 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 120 through 122 removed outlier: 6.827A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AA9, first strand: chain 'A' and resid 151 through 153 Processing sheet with id=AB1, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB2, first strand: chain 'A' and resid 281 through 282 Processing sheet with id=AB3, first strand: chain 'D' and resid 31 through 36 removed outlier: 3.690A pdb=" N ASN D 28 " --> pdb=" O GLY D 31 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 24 through 26 removed outlier: 4.091A pdb=" N ASP C 24 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AB6, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AB7, first strand: chain 'C' and resid 51 through 54 removed outlier: 5.953A pdb=" N LEU C 51 " --> pdb=" O ASP C 275 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N CYS C 277 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.568A pdb=" N LEU C 59 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE C 87 " --> pdb=" O ILE C 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.425A pdb=" N HIS C 101 " --> pdb=" O TYR C 232 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N TRP C 234 " --> pdb=" O HIS C 101 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.425A pdb=" N HIS C 101 " --> pdb=" O TYR C 232 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N TRP C 234 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N LEU C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 115 through 117 removed outlier: 7.434A pdb=" N SER C 261 " --> pdb=" O SER C 116 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AC4, first strand: chain 'C' and resid 164 through 169 removed outlier: 3.582A pdb=" N ALA C 247 " --> pdb=" O LEU C 164 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 286 through 287 Processing sheet with id=AC6, first strand: chain 'F' and resid 31 through 36 removed outlier: 6.499A pdb=" N CYS F 137 " --> pdb=" O ILE F 133 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 24 through 26 removed outlier: 4.186A pdb=" N ASP E 24 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 39 through 41 Processing sheet with id=AC9, first strand: chain 'E' and resid 43 through 44 Processing sheet with id=AD1, first strand: chain 'E' and resid 51 through 54 removed outlier: 6.376A pdb=" N LEU E 51 " --> pdb=" O ASP E 275 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N CYS E 277 " --> pdb=" O LEU E 51 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 59 through 61 removed outlier: 6.518A pdb=" N ILE E 87 " --> pdb=" O ILE E 268 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 115 through 121 Processing sheet with id=AD4, first strand: chain 'E' and resid 130 through 131 Processing sheet with id=AD5, first strand: chain 'E' and resid 151 through 153 Processing sheet with id=AD6, first strand: chain 'E' and resid 164 through 169 Processing sheet with id=AD7, first strand: chain 'E' and resid 286 through 288 removed outlier: 3.965A pdb=" N CYS E 281 " --> pdb=" O ILE E 288 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AD9, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.150A pdb=" N ASP H 33 " --> pdb=" O ASP H 95 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.121A pdb=" N VAL H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 9 through 12 removed outlier: 6.322A pdb=" N TRP I 35 " --> pdb=" O MET I 47 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 9 through 12 removed outlier: 5.997A pdb=" N LEU I 95A" --> pdb=" O ALA I 92 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 18 through 24 Processing sheet with id=AE5, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AE6, first strand: chain 'J' and resid 11 through 12 removed outlier: 4.124A pdb=" N ASP J 33 " --> pdb=" O ASP J 95 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 9 through 12 removed outlier: 3.516A pdb=" N ILE K 48 " --> pdb=" O TRP K 35 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLN K 37 " --> pdb=" O LEU K 46 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N LEU K 46 " --> pdb=" O GLN K 37 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 9 through 12 removed outlier: 6.351A pdb=" N LEU K 95A" --> pdb=" O ALA K 92 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 19 through 24 Processing sheet with id=AF1, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AF2, first strand: chain 'M' and resid 10 through 12 removed outlier: 4.183A pdb=" N ASP M 33 " --> pdb=" O ASP M 95 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N MET M 34 " --> pdb=" O GLY M 50 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N GLY M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'N' and resid 9 through 12 removed outlier: 6.512A pdb=" N TRP N 35 " --> pdb=" O MET N 47 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'N' and resid 9 through 12 removed outlier: 5.986A pdb=" N LEU N 95A" --> pdb=" O ALA N 92 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'N' and resid 18 through 24 699 hydrogen bonds defined for protein. 1860 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: 2.71 Time building geometry restraints manager: 1.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 5383 1.35 - 1.47: 4256 1.47 - 1.60: 7033 1.60 - 1.73: 0 1.73 - 1.86: 100 Bond restraints: 16772 Sorted by residual: bond pdb=" CA TYR A 161 " pdb=" C TYR A 161 " ideal model delta sigma weight residual 1.524 1.471 0.053 1.26e-02 6.30e+03 1.79e+01 bond pdb=" CA SER C 165 " pdb=" CB SER C 165 " ideal model delta sigma weight residual 1.528 1.481 0.047 1.13e-02 7.83e+03 1.76e+01 bond pdb=" CA SER E 203 " pdb=" CB SER E 203 " ideal model delta sigma weight residual 1.532 1.467 0.065 1.58e-02 4.01e+03 1.67e+01 bond pdb=" CA SER E 146 " pdb=" CB SER E 146 " ideal model delta sigma weight residual 1.532 1.477 0.055 1.45e-02 4.76e+03 1.44e+01 bond pdb=" CA TYR A 201 " pdb=" C TYR A 201 " ideal model delta sigma weight residual 1.520 1.475 0.045 1.22e-02 6.72e+03 1.37e+01 ... (remaining 16767 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 21778 1.77 - 3.54: 822 3.54 - 5.31: 159 5.31 - 7.08: 36 7.08 - 8.84: 14 Bond angle restraints: 22809 Sorted by residual: angle pdb=" N TRP D 21 " pdb=" CA TRP D 21 " pdb=" C TRP D 21 " ideal model delta sigma weight residual 113.97 105.65 8.32 1.28e+00 6.10e-01 4.23e+01 angle pdb=" N LEU E 194 " pdb=" CA LEU E 194 " pdb=" C LEU E 194 " ideal model delta sigma weight residual 112.04 104.56 7.48 1.44e+00 4.82e-01 2.70e+01 angle pdb=" CA HIS A 196 " pdb=" CB HIS A 196 " pdb=" CG HIS A 196 " ideal model delta sigma weight residual 113.80 108.81 4.99 1.00e+00 1.00e+00 2.49e+01 angle pdb=" N LEU C 320 " pdb=" CA LEU C 320 " pdb=" CB LEU C 320 " ideal model delta sigma weight residual 110.85 103.19 7.66 1.54e+00 4.22e-01 2.48e+01 angle pdb=" CA HIS D 25 " pdb=" CB HIS D 25 " pdb=" CG HIS D 25 " ideal model delta sigma weight residual 113.80 118.72 -4.92 1.00e+00 1.00e+00 2.42e+01 ... (remaining 22804 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 8658 17.97 - 35.93: 898 35.93 - 53.90: 261 53.90 - 71.87: 44 71.87 - 89.83: 8 Dihedral angle restraints: 9869 sinusoidal: 3663 harmonic: 6206 Sorted by residual: dihedral pdb=" CD ARG A 120 " pdb=" NE ARG A 120 " pdb=" CZ ARG A 120 " pdb=" NH1 ARG A 120 " ideal model delta sinusoidal sigma weight residual 0.00 -80.12 80.12 1 1.00e+01 1.00e-02 7.95e+01 dihedral pdb=" CD ARG B 75 " pdb=" NE ARG B 75 " pdb=" CZ ARG B 75 " pdb=" NH1 ARG B 75 " ideal model delta sinusoidal sigma weight residual 0.00 -68.73 68.73 1 1.00e+01 1.00e-02 6.12e+01 dihedral pdb=" CD ARG M 66 " pdb=" NE ARG M 66 " pdb=" CZ ARG M 66 " pdb=" NH1 ARG M 66 " ideal model delta sinusoidal sigma weight residual 0.00 53.43 -53.43 1 1.00e+01 1.00e-02 3.88e+01 ... (remaining 9866 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1946 0.053 - 0.105: 397 0.105 - 0.158: 108 0.158 - 0.211: 30 0.211 - 0.263: 11 Chirality restraints: 2492 Sorted by residual: chirality pdb=" CA LYS B 131 " pdb=" N LYS B 131 " pdb=" C LYS B 131 " pdb=" CB LYS B 131 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA TYR D 24 " pdb=" N TYR D 24 " pdb=" C TYR D 24 " pdb=" CB TYR D 24 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA HIS C 141 " pdb=" N HIS C 141 " pdb=" C HIS C 141 " pdb=" CB HIS C 141 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 2489 not shown) Planarity restraints: 2957 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 120 " -1.092 9.50e-02 1.11e+02 4.89e-01 1.44e+02 pdb=" NE ARG A 120 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG A 120 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 120 " -0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG A 120 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 75 " -1.050 9.50e-02 1.11e+02 4.71e-01 1.34e+02 pdb=" NE ARG B 75 " 0.062 2.00e-02 2.50e+03 pdb=" CZ ARG B 75 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG B 75 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 75 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG M 66 " -0.886 9.50e-02 1.11e+02 3.97e-01 9.57e+01 pdb=" NE ARG M 66 " 0.053 2.00e-02 2.50e+03 pdb=" CZ ARG M 66 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG M 66 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG M 66 " -0.024 2.00e-02 2.50e+03 ... (remaining 2954 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2686 2.76 - 3.30: 14228 3.30 - 3.83: 27316 3.83 - 4.37: 32543 4.37 - 4.90: 57183 Nonbonded interactions: 133956 Sorted by model distance: nonbonded pdb=" N ASP E 11 " pdb=" O GLN F 27 " model vdw 2.228 3.120 nonbonded pdb=" OG1 THR C 131 " pdb=" OG1 THR C 155 " model vdw 2.246 3.040 nonbonded pdb=" OE1 GLN E 111 " pdb=" NH2 ARG E 262 " model vdw 2.251 3.120 nonbonded pdb=" O SER M 29 " pdb=" NH2 ARG M 71 " model vdw 2.258 3.120 nonbonded pdb=" OH TYR I 39 " pdb=" O GLU I 81 " model vdw 2.269 3.040 ... (remaining 133951 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 11 through 74 or (resid 75 and (name N or name CA or name \ C or name O or name CB )) or resid 76 through 187 or (resid 188 and (name N or n \ ame CA or name C or name O or name CB )) or resid 189 through 224 or (resid 225 \ through 227 and (name N or name CA or name C or name O or name CB )) or resid 22 \ 8 through 262A or resid 265 through 273 or (resid 274 through 276 and (name N or \ name CA or name C or name O or name CB )) or resid 277 through 324)) selection = (chain 'C' and (resid 11 through 273 or (resid 274 through 276 and (name N or na \ me CA or name C or name O or name CB )) or resid 277 through 324)) selection = (chain 'E' and (resid 11 through 74 or (resid 75 and (name N or name CA or name \ C or name O or name CB )) or resid 76 through 187 or (resid 188 and (name N or n \ ame CA or name C or name O or name CB )) or resid 189 through 275 or (resid 276 \ and (name N or name CA or name C or name O or name CB )) or resid 277 through 32 \ 4)) } ncs_group { reference = (chain 'B' and (resid 2 through 61 or (resid 62 and (name N or name CA or name C \ or name O or name CB )) or resid 65 through 68 or (resid 69 and (name N or name \ CA or name C or name O or name CB )) or resid 70 through 142 or (resid 143 and \ (name N or name CA or name C or name O or name CB )) or resid 144 through 170)) selection = (chain 'D' and (resid 2 through 28 or (resid 29 and (name N or name CA or name C \ or name O or name CB )) or resid 30 through 68 or (resid 69 and (name N or name \ CA or name C or name O or name CB )) or resid 70 through 170)) selection = (chain 'F' and (resid 2 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 28 or (resid 29 and (name N or name \ CA or name C or name O or name CB )) or resid 30 through 61 or (resid 62 and (n \ ame N or name CA or name C or name O or name CB )) or resid 65 through 142 or (r \ esid 143 and (name N or name CA or name C or name O or name CB )) or resid 144 t \ hrough 170)) } ncs_group { reference = (chain 'H' and (resid 2 through 74 or (resid 75 and (name N or name CA or name C \ or name O or name CB )) or resid 76 through 104 or (resid 105 and (name N or na \ me CA or name C or name O or name CB )) or resid 106 through 113)) selection = chain 'J' selection = (chain 'M' and (resid 2 through 74 or (resid 75 and (name N or name CA or name C \ or name O or name CB )) or resid 76 through 113)) } ncs_group { reference = (chain 'I' and (resid 2 through 80 or (resid 81 and (name N or name CA or name C \ or name O or name CB )) or resid 82 or (resid 83 through 84 and (name N or name \ CA or name C or name O or name CB )) or resid 85 through 106)) selection = (chain 'K' and (resid 2 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB )) or resid 61 through 106)) selection = (chain 'N' and (resid 2 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB )) or resid 61 through 80 or (resid 81 and (name N or name \ CA or name C or name O or name CB )) or resid 82 through 106)) } 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 individual isotropic 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: 35.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.630 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.700 Find NCS groups from input model: 0.330 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: 0.010 Load rotamer database and sin/cos tables:5.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 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 : 0.005 0.065 16787 Z= 0.338 Angle : 0.798 8.845 22839 Z= 0.505 Chirality : 0.052 0.263 2492 Planarity : 0.020 0.489 2957 Dihedral : 15.955 89.835 5880 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.16 % Favored : 94.61 % Rotamer: Outliers : 2.90 % Allowed : 18.52 % Favored : 78.57 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % 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: -0.14 (0.18), residues: 2132 helix: 1.54 (0.28), residues: 371 sheet: 0.89 (0.25), residues: 451 loop : -0.98 (0.16), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 310 TYR 0.027 0.001 TYR D 24 PHE 0.016 0.002 PHE E 118 TRP 0.019 0.001 TRP F 21 HIS 0.008 0.001 HIS D 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.34 (16772) covalent geometry : angle 0.79736 / 0.50 (22809) SS BOND : bond 0.00286 / 0.16 ( 15) SS BOND : angle 0.97679 / 0.59 ( 30) hydrogen bonds : bond 0.13422 / 8.82 ( 672) hydrogen bonds : angle 6.13607 / 4.25 ( 1860) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 1861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 401 time to evaluate : 0.610 Fit side-chains revert: symmetry clash REVERT: A 53 LEU cc_start: 0.8241 (mt) cc_final: 0.8000 (mp) REVERT: A 56 ILE cc_start: 0.8473 (mm) cc_final: 0.8198 (mt) REVERT: B 132 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7608 (mp0) REVERT: B 137 CYS cc_start: 0.7174 (m) cc_final: 0.6925 (m) REVERT: B 150 GLU cc_start: 0.8024 (tp30) cc_final: 0.7716 (tp30) REVERT: B 161 LYS cc_start: 0.8606 (tttt) cc_final: 0.8364 (ttpp) REVERT: C 25 THR cc_start: 0.8309 (OUTLIER) cc_final: 0.7815 (p) REVERT: C 220 ARG cc_start: 0.7960 (mmm-85) cc_final: 0.7179 (mmm-85) REVERT: C 222 LYS cc_start: 0.8132 (ttmm) cc_final: 0.7870 (ttmm) REVERT: C 291 SER cc_start: 0.8619 (t) cc_final: 0.8277 (m) REVERT: C 298 HIS cc_start: 0.8856 (t-90) cc_final: 0.8634 (t70) REVERT: D 106 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.7658 (mtt-85) REVERT: D 116 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8430 (tttm) REVERT: D 152 VAL cc_start: 0.8663 (t) cc_final: 0.8444 (t) REVERT: E 23 THR cc_start: 0.8493 (p) cc_final: 0.8068 (t) REVERT: E 244 ILE cc_start: 0.8737 (mt) cc_final: 0.8449 (mm) REVERT: E 318 THR cc_start: 0.8614 (m) cc_final: 0.8184 (p) REVERT: F 135 ASN cc_start: 0.7214 (t0) cc_final: 0.6875 (t0) REVERT: F 150 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7570 (mm-30) REVERT: I 94 SER cc_start: 0.8693 (p) cc_final: 0.8442 (t) REVERT: J 21 SER cc_start: 0.8395 (m) cc_final: 0.8090 (t) REVERT: J 48 VAL cc_start: 0.8658 (t) cc_final: 0.8372 (p) REVERT: J 82 SER cc_start: 0.8499 (m) cc_final: 0.8163 (p) REVERT: K 22 SER cc_start: 0.8450 (m) cc_final: 0.8070 (p) REVERT: K 34 SER cc_start: 0.8537 (OUTLIER) cc_final: 0.8171 (p) REVERT: M 35 SER cc_start: 0.8545 (OUTLIER) cc_final: 0.8341 (p) REVERT: N 52 SER cc_start: 0.8520 (OUTLIER) cc_final: 0.8298 (m) outliers start: 50 outliers final: 21 residues processed: 424 average time/residue: 0.5614 time to fit residues: 265.1336 Evaluate side-chains 422 residues out of total 1861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 394 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain B residue 71 ASN Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 285 GLN Chi-restraints excluded: chain D residue 106 ARG Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain E residue 197 LYS Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 82 LYS Chi-restraints excluded: chain F residue 139 GLU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain M residue 35 SER Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 52 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.0030 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 0.9990 chunk 77 optimal weight: 0.0970 chunk 122 optimal weight: 0.6980 overall best weight: 0.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 ASN B 53 ASN B 125 GLN B 129 ASN C 196 HIS C 269 ASN C 322 ASN D 53 ASN E 269 ASN ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 125 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.124626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.111731 restraints weight = 23026.611| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.77 r_work: 0.3333 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.0723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16787 Z= 0.143 Angle : 0.520 9.097 22839 Z= 0.274 Chirality : 0.041 0.145 2492 Planarity : 0.004 0.049 2957 Dihedral : 5.795 86.497 2403 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.89 % Favored : 96.06 % Rotamer: Outliers : 2.61 % Allowed : 17.83 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.22 (0.18), residues: 2132 helix: 2.27 (0.27), residues: 363 sheet: 0.89 (0.25), residues: 457 loop : -0.78 (0.16), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 315 TYR 0.012 0.001 TYR D 24 PHE 0.014 0.002 PHE E 118 TRP 0.016 0.001 TRP F 21 HIS 0.008 0.001 HIS C 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (16772) covalent geometry : angle 0.51980 / 0.27 (22809) SS BOND : bond 0.00321 / 0.21 ( 15) SS BOND : angle 0.58282 / 0.35 ( 30) hydrogen bonds : bond 0.04409 / 2.97 ( 672) hydrogen bonds : angle 4.90092 / 3.45 ( 1860) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 1861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 392 time to evaluate : 0.805 Fit side-chains revert: symmetry clash REVERT: A 56 ILE cc_start: 0.8443 (mm) cc_final: 0.8160 (mt) REVERT: A 119 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.7052 (tt0) REVERT: B 50 ASN cc_start: 0.8252 (t0) cc_final: 0.8025 (t0) REVERT: B 150 GLU cc_start: 0.8048 (tp30) cc_final: 0.7735 (tp30) REVERT: B 161 LYS cc_start: 0.8563 (tttt) cc_final: 0.8323 (ttpp) REVERT: C 25 THR cc_start: 0.8257 (OUTLIER) cc_final: 0.7749 (p) REVERT: C 148 TYR cc_start: 0.8463 (m-80) cc_final: 0.8179 (m-80) REVERT: C 220 ARG cc_start: 0.7922 (mmm-85) cc_final: 0.7145 (mmm-85) REVERT: C 222 LYS cc_start: 0.8096 (ttmm) cc_final: 0.7846 (ttmm) REVERT: C 291 SER cc_start: 0.8598 (t) cc_final: 0.8252 (m) REVERT: C 298 HIS cc_start: 0.8866 (t-90) cc_final: 0.8615 (t70) REVERT: D 150 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7333 (mm-30) REVERT: E 23 THR cc_start: 0.8489 (p) cc_final: 0.8068 (t) REVERT: E 194 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7539 (tt) REVERT: E 318 THR cc_start: 0.8636 (m) cc_final: 0.8169 (p) REVERT: F 17 MET cc_start: 0.8458 (ptm) cc_final: 0.8248 (ttp) REVERT: F 150 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7613 (mm-30) REVERT: H 82 MET cc_start: 0.8058 (mtt) cc_final: 0.7774 (mtt) REVERT: I 94 SER cc_start: 0.8667 (p) cc_final: 0.8372 (t) REVERT: J 21 SER cc_start: 0.8388 (m) cc_final: 0.8081 (t) REVERT: J 48 VAL cc_start: 0.8665 (t) cc_final: 0.8375 (p) REVERT: J 82 SER cc_start: 0.8521 (m) cc_final: 0.8163 (p) REVERT: N 52 SER cc_start: 0.8529 (p) cc_final: 0.8269 (m) outliers start: 45 outliers final: 19 residues processed: 416 average time/residue: 0.5800 time to fit residues: 267.8089 Evaluate side-chains 410 residues out of total 1861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 388 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 79 SER Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 94 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 18 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 171 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 167 optimal weight: 0.5980 chunk 106 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 129 ASN A 295 GLN B 53 ASN B 125 GLN B 129 ASN C 269 ASN ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 170 ASN E 269 ASN ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 125 GLN J 31 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.124253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.111231 restraints weight = 23250.753| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.77 r_work: 0.3314 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.0903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 16787 Z= 0.213 Angle : 0.544 8.774 22839 Z= 0.284 Chirality : 0.042 0.144 2492 Planarity : 0.004 0.052 2957 Dihedral : 4.766 42.720 2359 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.94 % Favored : 96.01 % Rotamer: Outliers : 3.43 % Allowed : 17.94 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.20 (0.18), residues: 2132 helix: 2.26 (0.27), residues: 363 sheet: 0.84 (0.25), residues: 457 loop : -0.78 (0.16), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 315 TYR 0.014 0.001 TYR K 49 PHE 0.021 0.002 PHE E 118 TRP 0.017 0.001 TRP F 21 HIS 0.006 0.001 HIS C 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.21 (16772) covalent geometry : angle 0.54367 / 0.28 (22809) SS BOND : bond 0.00307 / 0.17 ( 15) SS BOND : angle 0.62032 / 0.37 ( 30) hydrogen bonds : bond 0.04693 / 3.18 ( 672) hydrogen bonds : angle 4.85022 / 3.42 ( 1860) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 1861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 384 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8298 (mp) REVERT: A 56 ILE cc_start: 0.8418 (mm) cc_final: 0.8137 (mt) REVERT: B 150 GLU cc_start: 0.8084 (tp30) cc_final: 0.7771 (tp30) REVERT: B 161 LYS cc_start: 0.8592 (tttt) cc_final: 0.8346 (ttpp) REVERT: C 25 THR cc_start: 0.8294 (OUTLIER) cc_final: 0.7899 (p) REVERT: C 220 ARG cc_start: 0.7967 (mmm-85) cc_final: 0.7157 (mmm-85) REVERT: C 222 LYS cc_start: 0.8116 (ttmm) cc_final: 0.7867 (ttmm) REVERT: C 291 SER cc_start: 0.8611 (t) cc_final: 0.8278 (m) REVERT: E 23 THR cc_start: 0.8499 (p) cc_final: 0.8073 (t) REVERT: E 106 GLU cc_start: 0.7617 (mp0) cc_final: 0.7348 (mp0) REVERT: E 244 ILE cc_start: 0.8779 (mt) cc_final: 0.8492 (mm) REVERT: E 318 THR cc_start: 0.8655 (m) cc_final: 0.8199 (p) REVERT: F 17 MET cc_start: 0.8518 (ptm) cc_final: 0.8303 (ttp) REVERT: F 149 MET cc_start: 0.8103 (mmt) cc_final: 0.7893 (mmp) REVERT: F 150 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7632 (mm-30) REVERT: I 94 SER cc_start: 0.8656 (p) cc_final: 0.8361 (t) REVERT: J 21 SER cc_start: 0.8422 (m) cc_final: 0.8112 (t) REVERT: J 48 VAL cc_start: 0.8686 (t) cc_final: 0.8405 (p) REVERT: J 82 SER cc_start: 0.8542 (m) cc_final: 0.8241 (p) REVERT: K 63 SER cc_start: 0.8405 (OUTLIER) cc_final: 0.8090 (p) REVERT: N 52 SER cc_start: 0.8586 (p) cc_final: 0.8340 (m) outliers start: 59 outliers final: 32 residues processed: 412 average time/residue: 0.5994 time to fit residues: 274.1599 Evaluate side-chains 420 residues out of total 1861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 385 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 321 ARG Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 102 THR Chi-restraints excluded: chain J residue 79 SER Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 62 SER Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 94 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 105 optimal weight: 0.8980 chunk 179 optimal weight: 3.9990 chunk 112 optimal weight: 0.7980 chunk 152 optimal weight: 0.7980 chunk 120 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 166 optimal weight: 2.9990 chunk 204 optimal weight: 0.0980 chunk 58 optimal weight: 0.9980 chunk 151 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 129 ASN A 196 HIS A 295 GLN B 53 ASN B 125 GLN C 269 ASN ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 170 ASN ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 125 GLN J 31 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.123098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.110105 restraints weight = 23004.011| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.78 r_work: 0.3317 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.0991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16787 Z= 0.186 Angle : 0.514 8.650 22839 Z= 0.271 Chirality : 0.042 0.141 2492 Planarity : 0.004 0.050 2957 Dihedral : 4.612 41.385 2356 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.85 % Favored : 96.11 % Rotamer: Outliers : 3.77 % Allowed : 17.89 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.32 (0.18), residues: 2132 helix: 2.36 (0.27), residues: 363 sheet: 0.90 (0.25), residues: 475 loop : -0.71 (0.17), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 315 TYR 0.012 0.001 TYR K 49 PHE 0.020 0.002 PHE E 118 TRP 0.018 0.001 TRP F 21 HIS 0.005 0.001 HIS C 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.19 (16772) covalent geometry : angle 0.51435 / 0.27 (22809) SS BOND : bond 0.00269 / 0.15 ( 15) SS BOND : angle 0.54806 / 0.33 ( 30) hydrogen bonds : bond 0.04419 / 2.99 ( 672) hydrogen bonds : angle 4.74468 / 3.35 ( 1860) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 1861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 385 time to evaluate : 0.648 Fit side-chains revert: symmetry clash REVERT: A 56 ILE cc_start: 0.8418 (mm) cc_final: 0.8134 (mt) REVERT: B 150 GLU cc_start: 0.8082 (tp30) cc_final: 0.7764 (tp30) REVERT: B 161 LYS cc_start: 0.8577 (tttt) cc_final: 0.8331 (ttpp) REVERT: C 25 THR cc_start: 0.8308 (OUTLIER) cc_final: 0.7876 (p) REVERT: C 125 LYS cc_start: 0.7759 (tppp) cc_final: 0.7468 (tppp) REVERT: C 194 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7449 (tp) REVERT: C 220 ARG cc_start: 0.7962 (mmm-85) cc_final: 0.7155 (mmm-85) REVERT: C 222 LYS cc_start: 0.8131 (ttmm) cc_final: 0.7881 (ttmm) REVERT: C 291 SER cc_start: 0.8600 (t) cc_final: 0.8262 (m) REVERT: C 321 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.7476 (mtp85) REVERT: D 152 VAL cc_start: 0.8686 (t) cc_final: 0.8437 (t) REVERT: E 23 THR cc_start: 0.8498 (p) cc_final: 0.8070 (t) REVERT: E 291 SER cc_start: 0.8475 (p) cc_final: 0.8261 (t) REVERT: E 315 ARG cc_start: 0.8765 (ttm-80) cc_final: 0.8455 (ttt90) REVERT: F 116 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8231 (tttm) REVERT: F 150 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7628 (mm-30) REVERT: H 82 MET cc_start: 0.8371 (mtp) cc_final: 0.8108 (mtm) REVERT: I 94 SER cc_start: 0.8639 (p) cc_final: 0.8360 (t) REVERT: J 21 SER cc_start: 0.8412 (m) cc_final: 0.8100 (t) REVERT: J 48 VAL cc_start: 0.8667 (t) cc_final: 0.8379 (p) REVERT: J 82 SER cc_start: 0.8535 (m) cc_final: 0.8245 (p) REVERT: K 63 SER cc_start: 0.8390 (OUTLIER) cc_final: 0.8080 (p) REVERT: N 52 SER cc_start: 0.8523 (p) cc_final: 0.8289 (m) outliers start: 65 outliers final: 36 residues processed: 421 average time/residue: 0.6131 time to fit residues: 286.4395 Evaluate side-chains 423 residues out of total 1861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 382 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 102 PHE Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 321 ARG Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 102 THR Chi-restraints excluded: chain J residue 79 SER Chi-restraints excluded: chain J residue 96 ARG Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 62 SER Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain N residue 9 SER Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 94 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 37 optimal weight: 0.9990 chunk 124 optimal weight: 0.3980 chunk 24 optimal weight: 1.9990 chunk 118 optimal weight: 0.5980 chunk 147 optimal weight: 0.8980 chunk 111 optimal weight: 0.8980 chunk 67 optimal weight: 0.4980 chunk 9 optimal weight: 0.9980 chunk 121 optimal weight: 0.4980 chunk 204 optimal weight: 0.0980 chunk 16 optimal weight: 0.7980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 129 ASN A 295 GLN B 53 ASN B 125 GLN C 269 ASN ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 170 ASN ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 125 GLN J 31 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.123316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.110317 restraints weight = 23099.940| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.79 r_work: 0.3327 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16787 Z= 0.132 Angle : 0.486 9.054 22839 Z= 0.255 Chirality : 0.041 0.136 2492 Planarity : 0.004 0.048 2957 Dihedral : 4.416 41.893 2355 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.43 % Allowed : 18.87 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.45 (0.18), residues: 2132 helix: 2.56 (0.27), residues: 363 sheet: 0.93 (0.25), residues: 475 loop : -0.63 (0.17), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 100 TYR 0.010 0.001 TYR C 201 PHE 0.016 0.001 PHE E 118 TRP 0.016 0.001 TRP F 21 HIS 0.004 0.001 HIS C 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (16772) covalent geometry : angle 0.48586 / 0.26 (22809) SS BOND : bond 0.00241 / 0.13 ( 15) SS BOND : angle 0.50637 / 0.31 ( 30) hydrogen bonds : bond 0.04068 / 2.76 ( 672) hydrogen bonds : angle 4.61851 / 3.27 ( 1860) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 1861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 383 time to evaluate : 0.657 Fit side-chains revert: symmetry clash REVERT: A 54 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8306 (mp) REVERT: A 56 ILE cc_start: 0.8435 (mm) cc_final: 0.8166 (mt) REVERT: A 102 PHE cc_start: 0.8282 (OUTLIER) cc_final: 0.7220 (m-80) REVERT: B 150 GLU cc_start: 0.8074 (tp30) cc_final: 0.7773 (tp30) REVERT: B 161 LYS cc_start: 0.8540 (tttt) cc_final: 0.8291 (ttpp) REVERT: C 25 THR cc_start: 0.8299 (OUTLIER) cc_final: 0.7842 (p) REVERT: C 125 LYS cc_start: 0.7769 (tppp) cc_final: 0.7471 (tppp) REVERT: C 194 LEU cc_start: 0.7646 (OUTLIER) cc_final: 0.7444 (tp) REVERT: C 220 ARG cc_start: 0.7928 (mmm-85) cc_final: 0.7138 (mmm-85) REVERT: C 222 LYS cc_start: 0.8127 (ttmm) cc_final: 0.7876 (ttmm) REVERT: C 291 SER cc_start: 0.8589 (t) cc_final: 0.8256 (m) REVERT: D 116 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8450 (tttm) REVERT: D 152 VAL cc_start: 0.8671 (t) cc_final: 0.8403 (t) REVERT: E 23 THR cc_start: 0.8494 (p) cc_final: 0.8071 (t) REVERT: E 106 GLU cc_start: 0.7597 (mp0) cc_final: 0.7337 (mp0) REVERT: E 291 SER cc_start: 0.8467 (p) cc_final: 0.8248 (t) REVERT: F 116 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8225 (tttm) REVERT: F 150 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7659 (mm-30) REVERT: I 94 SER cc_start: 0.8626 (p) cc_final: 0.8360 (t) REVERT: J 21 SER cc_start: 0.8394 (m) cc_final: 0.8084 (t) REVERT: J 48 VAL cc_start: 0.8658 (t) cc_final: 0.8366 (p) REVERT: J 82 SER cc_start: 0.8533 (m) cc_final: 0.8185 (p) REVERT: K 63 SER cc_start: 0.8380 (OUTLIER) cc_final: 0.8080 (p) outliers start: 59 outliers final: 38 residues processed: 413 average time/residue: 0.5802 time to fit residues: 266.6024 Evaluate side-chains 425 residues out of total 1861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 380 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 102 PHE Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 102 THR Chi-restraints excluded: chain J residue 79 SER Chi-restraints excluded: chain J residue 96 ARG Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain N residue 9 SER Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 94 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 64 optimal weight: 2.9990 chunk 152 optimal weight: 0.9980 chunk 147 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 115 optimal weight: 0.5980 chunk 157 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 201 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 129 ASN B 50 ASN C 269 ASN D 50 ASN E 170 ASN E 269 ASN F 125 GLN J 31 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.121478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.108464 restraints weight = 23006.944| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.77 r_work: 0.3288 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.085 16787 Z= 0.345 Angle : 0.606 8.809 22839 Z= 0.316 Chirality : 0.046 0.161 2492 Planarity : 0.005 0.057 2957 Dihedral : 4.927 45.939 2355 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 4.07 % Allowed : 18.47 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.06 (0.18), residues: 2132 helix: 2.04 (0.27), residues: 364 sheet: 0.78 (0.25), residues: 446 loop : -0.84 (0.16), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 100 TYR 0.021 0.002 TYR K 49 PHE 0.035 0.003 PHE E 118 TRP 0.019 0.002 TRP F 21 HIS 0.008 0.001 HIS C 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00799 / 0.35 (16772) covalent geometry : angle 0.60615 / 0.32 (22809) SS BOND : bond 0.00398 / 0.22 ( 15) SS BOND : angle 0.68575 / 0.41 ( 30) hydrogen bonds : bond 0.05136 / 3.49 ( 672) hydrogen bonds : angle 4.88177 / 3.45 ( 1860) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 1861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 378 time to evaluate : 0.658 Fit side-chains revert: symmetry clash REVERT: A 54 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8333 (mp) REVERT: A 56 ILE cc_start: 0.8409 (mm) cc_final: 0.8118 (mt) REVERT: B 150 GLU cc_start: 0.8112 (tp30) cc_final: 0.7810 (tp30) REVERT: B 161 LYS cc_start: 0.8616 (tttt) cc_final: 0.8371 (ttpp) REVERT: C 25 THR cc_start: 0.8301 (OUTLIER) cc_final: 0.7910 (p) REVERT: C 125 LYS cc_start: 0.7830 (OUTLIER) cc_final: 0.7523 (tppp) REVERT: C 194 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7559 (mp) REVERT: C 220 ARG cc_start: 0.8023 (mmm-85) cc_final: 0.7181 (mmm-85) REVERT: C 222 LYS cc_start: 0.8144 (ttmm) cc_final: 0.7894 (ttmm) REVERT: C 291 SER cc_start: 0.8642 (t) cc_final: 0.8321 (m) REVERT: C 321 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.7633 (mtp85) REVERT: D 106 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7693 (mtt-85) REVERT: D 116 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8465 (tttm) REVERT: E 23 THR cc_start: 0.8498 (p) cc_final: 0.8057 (t) REVERT: E 318 THR cc_start: 0.8617 (m) cc_final: 0.8228 (p) REVERT: F 17 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.8288 (ttp) REVERT: F 116 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8300 (tttm) REVERT: F 150 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7657 (mm-30) REVERT: I 94 SER cc_start: 0.8666 (p) cc_final: 0.8369 (t) REVERT: J 21 SER cc_start: 0.8444 (m) cc_final: 0.8137 (t) REVERT: J 82 SER cc_start: 0.8552 (m) cc_final: 0.8245 (p) REVERT: K 63 SER cc_start: 0.8398 (OUTLIER) cc_final: 0.8071 (p) REVERT: M 52 SER cc_start: 0.8220 (t) cc_final: 0.7889 (p) REVERT: N 52 SER cc_start: 0.8643 (p) cc_final: 0.8404 (m) outliers start: 70 outliers final: 42 residues processed: 415 average time/residue: 0.6228 time to fit residues: 285.4995 Evaluate side-chains 433 residues out of total 1861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 381 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 125 LYS Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 321 ARG Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 106 ARG Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 17 MET Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain J residue 96 ARG Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain M residue 62 SER Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 9 SER Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 94 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 180 optimal weight: 1.9990 chunk 40 optimal weight: 0.4980 chunk 52 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 200 optimal weight: 4.9990 chunk 147 optimal weight: 0.7980 chunk 94 optimal weight: 0.3980 chunk 155 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 82 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 129 ASN A 295 GLN C 269 ASN D 50 ASN D 125 GLN E 170 ASN E 269 ASN ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 125 GLN H 100EGLN J 31 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.123039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.110064 restraints weight = 22904.318| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.78 r_work: 0.3316 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16787 Z= 0.165 Angle : 0.519 8.612 22839 Z= 0.272 Chirality : 0.042 0.144 2492 Planarity : 0.004 0.049 2957 Dihedral : 4.659 45.304 2355 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.25 % Allowed : 19.98 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.26 (0.18), residues: 2132 helix: 2.36 (0.27), residues: 363 sheet: 0.81 (0.25), residues: 475 loop : -0.74 (0.17), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 229 TYR 0.011 0.001 TYR K 49 PHE 0.023 0.002 PHE E 118 TRP 0.020 0.001 TRP F 21 HIS 0.005 0.001 HIS C 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (16772) covalent geometry : angle 0.51896 / 0.27 (22809) SS BOND : bond 0.00253 / 0.14 ( 15) SS BOND : angle 0.51672 / 0.31 ( 30) hydrogen bonds : bond 0.04385 / 2.97 ( 672) hydrogen bonds : angle 4.72659 / 3.35 ( 1860) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 1861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 383 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 LEU cc_start: 0.8317 (mt) cc_final: 0.8041 (mp) REVERT: A 54 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8269 (mp) REVERT: A 56 ILE cc_start: 0.8428 (mm) cc_final: 0.8153 (mt) REVERT: B 132 GLU cc_start: 0.7765 (mp0) cc_final: 0.7508 (mp0) REVERT: B 150 GLU cc_start: 0.8094 (tp30) cc_final: 0.7793 (tp30) REVERT: B 161 LYS cc_start: 0.8574 (tttt) cc_final: 0.8323 (ttpp) REVERT: C 25 THR cc_start: 0.8301 (OUTLIER) cc_final: 0.7874 (p) REVERT: C 118 PHE cc_start: 0.7680 (OUTLIER) cc_final: 0.6854 (p90) REVERT: C 125 LYS cc_start: 0.7801 (OUTLIER) cc_final: 0.7445 (tppp) REVERT: C 194 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7543 (mp) REVERT: C 220 ARG cc_start: 0.7998 (mmm-85) cc_final: 0.7200 (mmm-85) REVERT: C 222 LYS cc_start: 0.8145 (ttmm) cc_final: 0.7895 (ttmm) REVERT: C 291 SER cc_start: 0.8600 (t) cc_final: 0.8276 (m) REVERT: D 106 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7655 (mtt-85) REVERT: D 116 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8447 (tttm) REVERT: D 152 VAL cc_start: 0.8669 (t) cc_final: 0.8436 (t) REVERT: E 23 THR cc_start: 0.8489 (p) cc_final: 0.8057 (t) REVERT: E 244 ILE cc_start: 0.8771 (mt) cc_final: 0.8489 (mm) REVERT: E 318 THR cc_start: 0.8594 (m) cc_final: 0.8169 (p) REVERT: F 116 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8237 (tttm) REVERT: F 150 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7659 (mm-30) REVERT: I 94 SER cc_start: 0.8624 (p) cc_final: 0.8353 (t) REVERT: J 21 SER cc_start: 0.8426 (m) cc_final: 0.8102 (t) REVERT: J 48 VAL cc_start: 0.8658 (t) cc_final: 0.8383 (p) REVERT: J 82 SER cc_start: 0.8546 (m) cc_final: 0.8244 (p) REVERT: K 63 SER cc_start: 0.8390 (OUTLIER) cc_final: 0.8076 (p) outliers start: 56 outliers final: 38 residues processed: 413 average time/residue: 0.6058 time to fit residues: 277.3379 Evaluate side-chains 430 residues out of total 1861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 383 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 102 PHE Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 125 LYS Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 321 ARG Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 106 ARG Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain J residue 96 ARG Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 9 SER Chi-restraints excluded: chain N residue 30 TYR Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 94 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 135 optimal weight: 0.9980 chunk 197 optimal weight: 0.7980 chunk 185 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 184 optimal weight: 5.9990 chunk 84 optimal weight: 0.4980 chunk 3 optimal weight: 0.6980 chunk 13 optimal weight: 4.9990 chunk 162 optimal weight: 4.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 295 GLN B 53 ASN C 269 ASN D 50 ASN E 170 ASN ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 125 GLN J 31 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.122441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.109402 restraints weight = 22960.718| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.78 r_work: 0.3308 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 16787 Z= 0.207 Angle : 0.535 8.708 22839 Z= 0.280 Chirality : 0.042 0.153 2492 Planarity : 0.004 0.049 2957 Dihedral : 4.686 46.206 2355 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.08 % Allowed : 20.21 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.25 (0.18), residues: 2132 helix: 2.33 (0.27), residues: 363 sheet: 0.78 (0.24), residues: 475 loop : -0.74 (0.17), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 100 TYR 0.013 0.001 TYR K 49 PHE 0.026 0.002 PHE E 118 TRP 0.018 0.001 TRP F 21 HIS 0.006 0.001 HIS C 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.21 (16772) covalent geometry : angle 0.53518 / 0.28 (22809) SS BOND : bond 0.00291 / 0.16 ( 15) SS BOND : angle 0.55079 / 0.33 ( 30) hydrogen bonds : bond 0.04496 / 3.05 ( 672) hydrogen bonds : angle 4.72099 / 3.34 ( 1860) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 1861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 384 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8266 (mp) REVERT: A 56 ILE cc_start: 0.8427 (mm) cc_final: 0.8152 (mt) REVERT: B 132 GLU cc_start: 0.7760 (mp0) cc_final: 0.7505 (mp0) REVERT: B 150 GLU cc_start: 0.8098 (tp30) cc_final: 0.7800 (tp30) REVERT: B 161 LYS cc_start: 0.8581 (tttt) cc_final: 0.8329 (ttpp) REVERT: C 25 THR cc_start: 0.8312 (OUTLIER) cc_final: 0.7901 (p) REVERT: C 118 PHE cc_start: 0.7693 (OUTLIER) cc_final: 0.6872 (p90) REVERT: C 125 LYS cc_start: 0.7807 (OUTLIER) cc_final: 0.7452 (tppp) REVERT: C 194 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7597 (mp) REVERT: C 220 ARG cc_start: 0.7991 (mmm-85) cc_final: 0.7172 (mmm-85) REVERT: C 222 LYS cc_start: 0.8150 (ttmm) cc_final: 0.7900 (ttmm) REVERT: C 291 SER cc_start: 0.8604 (t) cc_final: 0.8279 (m) REVERT: D 106 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.7660 (mtt-85) REVERT: D 116 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8472 (tttm) REVERT: D 152 VAL cc_start: 0.8676 (t) cc_final: 0.8443 (t) REVERT: E 23 THR cc_start: 0.8488 (p) cc_final: 0.8054 (t) REVERT: E 244 ILE cc_start: 0.8770 (mt) cc_final: 0.8490 (mm) REVERT: E 318 THR cc_start: 0.8614 (m) cc_final: 0.8197 (p) REVERT: F 116 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8241 (tttm) REVERT: F 150 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7654 (mm-30) REVERT: I 94 SER cc_start: 0.8635 (p) cc_final: 0.8362 (t) REVERT: J 21 SER cc_start: 0.8421 (m) cc_final: 0.8101 (t) REVERT: J 48 VAL cc_start: 0.8673 (t) cc_final: 0.8386 (p) REVERT: J 82 SER cc_start: 0.8557 (m) cc_final: 0.8261 (p) REVERT: K 63 SER cc_start: 0.8397 (OUTLIER) cc_final: 0.8082 (p) outliers start: 53 outliers final: 38 residues processed: 410 average time/residue: 0.5266 time to fit residues: 239.6679 Evaluate side-chains 425 residues out of total 1861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 378 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 102 PHE Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 125 LYS Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 321 ARG Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 106 ARG Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain J residue 96 ARG Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain M residue 62 SER Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 9 SER Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 94 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 179 optimal weight: 6.9990 chunk 49 optimal weight: 0.9980 chunk 92 optimal weight: 0.1980 chunk 208 optimal weight: 1.9990 chunk 145 optimal weight: 0.4980 chunk 121 optimal weight: 0.0010 chunk 26 optimal weight: 0.0030 chunk 104 optimal weight: 0.8980 chunk 105 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 190 optimal weight: 0.6980 overall best weight: 0.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 129 ASN A 295 GLN C 269 ASN D 50 ASN E 170 ASN F 125 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.123899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.110982 restraints weight = 23040.906| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.78 r_work: 0.3337 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16787 Z= 0.109 Angle : 0.479 8.474 22839 Z= 0.251 Chirality : 0.040 0.140 2492 Planarity : 0.004 0.047 2957 Dihedral : 4.372 44.528 2355 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.61 % Allowed : 20.85 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.45 (0.18), residues: 2132 helix: 2.58 (0.27), residues: 371 sheet: 0.88 (0.25), residues: 473 loop : -0.64 (0.17), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 100 TYR 0.012 0.001 TYR C 201 PHE 0.018 0.001 PHE E 118 TRP 0.020 0.001 TRP F 21 HIS 0.003 0.001 HIS C 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (16772) covalent geometry : angle 0.47889 / 0.25 (22809) SS BOND : bond 0.00223 / 0.13 ( 15) SS BOND : angle 0.50029 / 0.31 ( 30) hydrogen bonds : bond 0.03816 / 2.58 ( 672) hydrogen bonds : angle 4.53842 / 3.22 ( 1860) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 1861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 382 time to evaluate : 0.647 Fit side-chains revert: symmetry clash REVERT: A 53 LEU cc_start: 0.8240 (mt) cc_final: 0.7954 (mp) REVERT: A 54 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8276 (mp) REVERT: A 56 ILE cc_start: 0.8459 (mm) cc_final: 0.8194 (mt) REVERT: A 102 PHE cc_start: 0.8259 (OUTLIER) cc_final: 0.7175 (m-80) REVERT: B 50 ASN cc_start: 0.8268 (t0) cc_final: 0.8047 (t0) REVERT: B 132 GLU cc_start: 0.7726 (mp0) cc_final: 0.7475 (mp0) REVERT: B 150 GLU cc_start: 0.8059 (tp30) cc_final: 0.7766 (tp30) REVERT: B 161 LYS cc_start: 0.8532 (tttt) cc_final: 0.8294 (ttpp) REVERT: C 25 THR cc_start: 0.8265 (OUTLIER) cc_final: 0.7765 (p) REVERT: C 118 PHE cc_start: 0.7574 (OUTLIER) cc_final: 0.6828 (p90) REVERT: C 125 LYS cc_start: 0.7787 (OUTLIER) cc_final: 0.7477 (tppp) REVERT: C 194 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7542 (mp) REVERT: C 220 ARG cc_start: 0.7922 (mmm-85) cc_final: 0.7130 (mmm-85) REVERT: C 222 LYS cc_start: 0.8137 (ttmm) cc_final: 0.7886 (ttmm) REVERT: C 242 THR cc_start: 0.8309 (OUTLIER) cc_final: 0.7917 (m) REVERT: C 291 SER cc_start: 0.8589 (t) cc_final: 0.8255 (m) REVERT: C 298 HIS cc_start: 0.8863 (t-90) cc_final: 0.8635 (t70) REVERT: D 116 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8436 (tttm) REVERT: D 152 VAL cc_start: 0.8635 (t) cc_final: 0.8434 (t) REVERT: E 23 THR cc_start: 0.8484 (p) cc_final: 0.8069 (t) REVERT: E 244 ILE cc_start: 0.8756 (mt) cc_final: 0.8465 (mm) REVERT: E 318 THR cc_start: 0.8563 (m) cc_final: 0.8104 (p) REVERT: F 116 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8237 (tttm) REVERT: F 150 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7670 (mm-30) REVERT: I 94 SER cc_start: 0.8602 (p) cc_final: 0.8339 (t) REVERT: J 21 SER cc_start: 0.8381 (m) cc_final: 0.8065 (t) REVERT: J 48 VAL cc_start: 0.8642 (t) cc_final: 0.8366 (p) REVERT: J 82 SER cc_start: 0.8562 (m) cc_final: 0.8283 (p) REVERT: K 22 SER cc_start: 0.8438 (m) cc_final: 0.8079 (p) REVERT: K 63 SER cc_start: 0.8365 (OUTLIER) cc_final: 0.8066 (p) outliers start: 45 outliers final: 28 residues processed: 407 average time/residue: 0.6153 time to fit residues: 277.6825 Evaluate side-chains 416 residues out of total 1861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 378 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 102 PHE Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 125 LYS Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 30 TYR Chi-restraints excluded: chain J residue 96 ARG Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 9 SER Chi-restraints excluded: chain N residue 94 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 127 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 201 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 162 optimal weight: 4.9990 chunk 125 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 123 optimal weight: 0.7980 chunk 188 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 53 ASN C 269 ASN E 269 ASN F 125 GLN H 100EGLN J 31 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.121788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.108704 restraints weight = 22973.076| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.79 r_work: 0.3305 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 16787 Z= 0.237 Angle : 0.555 8.693 22839 Z= 0.288 Chirality : 0.043 0.159 2492 Planarity : 0.004 0.050 2957 Dihedral : 4.656 46.383 2355 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.50 % Allowed : 21.37 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.23 (0.18), residues: 2132 helix: 2.35 (0.27), residues: 364 sheet: 0.75 (0.25), residues: 455 loop : -0.73 (0.17), residues: 1313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 100 TYR 0.015 0.002 TYR K 49 PHE 0.028 0.002 PHE E 118 TRP 0.017 0.002 TRP F 21 HIS 0.006 0.001 HIS C 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00550 / 0.24 (16772) covalent geometry : angle 0.55476 / 0.29 (22809) SS BOND : bond 0.00309 / 0.17 ( 15) SS BOND : angle 0.59866 / 0.36 ( 30) hydrogen bonds : bond 0.04577 / 3.10 ( 672) hydrogen bonds : angle 4.67849 / 3.31 ( 1860) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 379 time to evaluate : 0.693 Fit side-chains revert: symmetry clash REVERT: A 53 LEU cc_start: 0.8310 (mt) cc_final: 0.8057 (mp) REVERT: A 54 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8323 (mp) REVERT: A 56 ILE cc_start: 0.8428 (mm) cc_final: 0.8146 (mt) REVERT: B 150 GLU cc_start: 0.8077 (tp30) cc_final: 0.7779 (tp30) REVERT: B 161 LYS cc_start: 0.8579 (tttt) cc_final: 0.8328 (ttpp) REVERT: C 25 THR cc_start: 0.8312 (OUTLIER) cc_final: 0.7891 (p) REVERT: C 118 PHE cc_start: 0.7683 (OUTLIER) cc_final: 0.6843 (p90) REVERT: C 125 LYS cc_start: 0.7798 (OUTLIER) cc_final: 0.7462 (tppp) REVERT: C 194 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7628 (mp) REVERT: C 220 ARG cc_start: 0.7991 (mmm-85) cc_final: 0.7172 (mmm-85) REVERT: C 222 LYS cc_start: 0.8165 (ttmm) cc_final: 0.7911 (ttmm) REVERT: C 242 THR cc_start: 0.8359 (OUTLIER) cc_final: 0.7967 (m) REVERT: C 291 SER cc_start: 0.8613 (t) cc_final: 0.8291 (m) REVERT: D 116 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8470 (tttm) REVERT: D 150 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7389 (mm-30) REVERT: D 152 VAL cc_start: 0.8677 (t) cc_final: 0.8458 (t) REVERT: E 23 THR cc_start: 0.8496 (p) cc_final: 0.8058 (t) REVERT: E 244 ILE cc_start: 0.8766 (mt) cc_final: 0.8479 (mm) REVERT: E 318 THR cc_start: 0.8629 (m) cc_final: 0.8198 (p) REVERT: F 116 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8255 (tttm) REVERT: F 150 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7647 (mm-30) REVERT: I 94 SER cc_start: 0.8637 (p) cc_final: 0.8364 (t) REVERT: J 21 SER cc_start: 0.8429 (m) cc_final: 0.8115 (t) REVERT: J 48 VAL cc_start: 0.8691 (t) cc_final: 0.8411 (p) REVERT: J 82 SER cc_start: 0.8555 (m) cc_final: 0.8260 (p) REVERT: K 63 SER cc_start: 0.8390 (OUTLIER) cc_final: 0.8072 (p) REVERT: M 52 SER cc_start: 0.8208 (t) cc_final: 0.7863 (p) outliers start: 43 outliers final: 24 residues processed: 401 average time/residue: 0.6579 time to fit residues: 290.5323 Evaluate side-chains 404 residues out of total 1861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 371 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 125 LYS Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain J residue 96 ARG Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain M residue 62 SER Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 9 SER Chi-restraints excluded: chain N residue 94 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 40 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 170 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 154 optimal weight: 0.0770 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 129 ASN C 269 ASN E 170 ASN E 269 ASN F 125 GLN J 31 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.123281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.110281 restraints weight = 22869.405| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.79 r_work: 0.3319 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16787 Z= 0.166 Angle : 0.524 8.876 22839 Z= 0.272 Chirality : 0.042 0.161 2492 Planarity : 0.004 0.048 2957 Dihedral : 4.547 44.570 2355 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.38 % Allowed : 21.43 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.34 (0.18), residues: 2132 helix: 2.35 (0.27), residues: 371 sheet: 0.83 (0.24), residues: 475 loop : -0.67 (0.17), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 100 TYR 0.012 0.001 TYR A 17 PHE 0.024 0.002 PHE E 118 TRP 0.019 0.001 TRP F 21 HIS 0.005 0.001 HIS C 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 (16772) covalent geometry : angle 0.52443 / 0.27 (22809) SS BOND : bond 0.00262 / 0.14 ( 15) SS BOND : angle 0.53457 / 0.32 ( 30) hydrogen bonds : bond 0.04226 / 2.86 ( 672) hydrogen bonds : angle 4.63203 / 3.28 ( 1860) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7448.84 seconds wall clock time: 127 minutes 43.34 seconds (7663.34 seconds total)