Starting phenix.real_space_refine on Thu Sep 18 07:33:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ei9_48079/09_2025/9ei9_48079.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ei9_48079/09_2025/9ei9_48079.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ei9_48079/09_2025/9ei9_48079.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ei9_48079/09_2025/9ei9_48079.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ei9_48079/09_2025/9ei9_48079.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ei9_48079/09_2025/9ei9_48079.map" } resolution = 3.89 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= 0.002 sd= 0.050 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 60 5.16 5 C 8988 2.51 5 N 2588 2.21 5 O 2928 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14564 Number of models: 1 Model: "" Number of chains: 23 Chain: "B" Number of atoms: 2552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2552 Classifications: {'peptide': 326} Link IDs: {'PTRANS': 20, 'TRANS': 305} Chain: "C" Number of atoms: 2537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2537 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 19, 'TRANS': 304} Chain: "E" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1385 Classifications: {'peptide': 172} Link IDs: {'TRANS': 171} Chain: "F" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1385 Classifications: {'peptide': 172} Link IDs: {'CIS': 1, 'TRANS': 170} Chain: "G" Number of atoms: 2548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2548 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 19, 'TRANS': 305} Chain: "I" Number of atoms: 1373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1373 Classifications: {'peptide': 170} Link IDs: {'TRANS': 169} Chain: "A" Number of atoms: 593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 593 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 101} Link IDs: {'PTRANS': 4, 'TRANS': 116} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 369 Unresolved non-hydrogen angles: 483 Unresolved non-hydrogen dihedrals: 323 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 3, 'PHE:plan': 5, 'TRP:plan': 5, 'ARG:plan': 3, 'HIS:plan': 2, 'ASP:plan': 7, 'ASN:plan1': 5, 'TYR:plan': 5} Unresolved non-hydrogen planarities: 203 Chain: "D" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 537 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 3, 'TRANS': 106} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 287 Unresolved non-hydrogen angles: 378 Unresolved non-hydrogen dihedrals: 236 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 3, 'TYR:plan': 3, 'TRP:plan': 2, 'ASP:plan': 4, 'HIS:plan': 2, 'PHE:plan': 5} Unresolved non-hydrogen planarities: 139 Chain: "H" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 603 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'PTRANS': 4, 'TRANS': 118} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 370 Unresolved non-hydrogen angles: 484 Unresolved non-hydrogen dihedrals: 324 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 3, 'PHE:plan': 5, 'TRP:plan': 5, 'ARG:plan': 3, 'HIS:plan': 2, 'ASP:plan': 7, 'ASN:plan1': 5, 'TYR:plan': 5} Unresolved non-hydrogen planarities: 203 Chain: "J" Number of atoms: 542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 542 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 89} Link IDs: {'PTRANS': 3, 'TRANS': 107} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 291 Unresolved non-hydrogen angles: 383 Unresolved non-hydrogen dihedrals: 239 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 3, 'TYR:plan': 3, 'TRP:plan': 2, 'ASP:plan': 4, 'HIS:plan': 2, 'PHE:plan': 5} Unresolved non-hydrogen planarities: 143 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "I" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.09, per 1000 atoms: 0.28 Number of scatterers: 14564 At special positions: 0 Unit cell: (98.7436, 109.477, 187.828, 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 60 16.00 O 2928 8.00 N 2588 7.00 C 8988 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS B 14 " - pdb=" SG CYS E 137 " distance=2.03 Simple disulfide: pdb=" SG CYS B 30 " - pdb=" SG CYS F 47 " distance=2.03 Simple disulfide: pdb=" SG CYS B 52 " - pdb=" SG CYS B 277 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 76 " distance=2.03 Simple disulfide: pdb=" SG CYS B 97 " - pdb=" SG CYS B 139 " distance=2.03 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 305 " distance=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS F 137 " distance=2.03 Simple disulfide: pdb=" SG CYS C 30 " - pdb=" SG CYS I 47 " distance=2.03 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " 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 47 " - pdb=" SG CYS G 30 " distance=2.04 Simple disulfide: pdb=" SG CYS E 144 " - pdb=" SG CYS E 148 " distance=2.03 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 148 " distance=2.02 Simple disulfide: pdb=" SG CYS G 14 " - pdb=" SG CYS I 137 " distance=2.03 Simple disulfide: pdb=" SG CYS G 52 " - pdb=" SG CYS G 277 " distance=2.03 Simple disulfide: pdb=" SG CYS G 64 " - pdb=" SG CYS G 76 " distance=2.03 Simple disulfide: pdb=" SG CYS G 97 " - pdb=" SG CYS G 139 " distance=2.03 Simple disulfide: pdb=" SG CYS G 281 " - pdb=" SG CYS G 305 " distance=2.03 Simple disulfide: pdb=" SG CYS I 144 " - pdb=" SG CYS I 148 " 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 Links applied BETA1-4 " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " NAG-ASN " NAG B 401 " - " ASN B 285 " " NAG B 402 " - " ASN B 133 " " NAG B 403 " - " ASN B 22 " " NAG B 404 " - " ASN B 38 " " NAG B 405 " - " ASN B 63 " " NAG C 401 " - " ASN C 285 " " NAG C 402 " - " ASN C 133 " " NAG C 403 " - " ASN C 22 " " NAG C 404 " - " ASN C 38 " " NAG C 405 " - " ASN C 63 " " NAG C 406 " - " ASN C 126 " " NAG E 301 " - " ASN E 154 " " NAG F 301 " - " ASN F 154 " " NAG G 401 " - " ASN G 285 " " NAG G 402 " - " ASN G 133 " " NAG G 403 " - " ASN G 22 " " NAG G 404 " - " ASN G 38 " " NAG G 405 " - " ASN G 63 " " NAG G 406 " - " ASN G 126 " " NAG I 301 " - " ASN I 154 " " NAG K 1 " - " ASN B 246 " " NAG L 1 " - " ASN B 165 " " NAG M 1 " - " ASN B 8 " " NAG N 1 " - " ASN C 246 " " NAG O 1 " - " ASN C 165 " " NAG P 1 " - " ASN G 246 " " NAG Q 1 " - " ASN G 165 " Time building additional restraints: 1.29 Conformation dependent library (CDL) restraints added in 562.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3588 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 44 sheets defined 20.7% alpha, 25.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'B' and resid 65 through 72 Processing helix chain 'B' and resid 76 through 80 removed outlier: 3.792A pdb=" N GLN B 80 " --> pdb=" O ASP B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 116 Processing helix chain 'B' and resid 187 through 196 Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 73 through 77 Processing helix chain 'C' and resid 104 through 116 removed outlier: 3.531A pdb=" N LEU C 108 " --> pdb=" O ASP C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'E' and resid 40 through 56 removed outlier: 3.750A pdb=" N CYS E 47 " --> pdb=" O ALA E 43 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE E 48 " --> pdb=" O ALA E 44 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG E 54 " --> pdb=" O GLY E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 126 removed outlier: 3.532A pdb=" N GLU E 85 " --> pdb=" O GLU E 81 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS E 88 " --> pdb=" O VAL E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 155 removed outlier: 3.562A pdb=" N ILE E 152 " --> pdb=" O CYS E 148 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG E 153 " --> pdb=" O ILE E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 169 removed outlier: 3.706A pdb=" N ASN E 168 " --> pdb=" O ASP E 164 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN E 169 " --> pdb=" O GLU E 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 56 removed outlier: 3.912A pdb=" N ALA F 43 " --> pdb=" O LYS F 39 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA F 44 " --> pdb=" O SER F 40 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG F 54 " --> pdb=" O GLY F 50 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU F 55 " --> pdb=" O LYS F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 125 removed outlier: 3.773A pdb=" N GLN F 105 " --> pdb=" O ALA F 101 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU F 118 " --> pdb=" O GLU F 114 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR F 122 " --> pdb=" O LEU F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 155 removed outlier: 3.687A pdb=" N ILE F 149 " --> pdb=" O ASP F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 172 removed outlier: 3.596A pdb=" N LEU F 167 " --> pdb=" O ARG F 163 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ASN F 168 " --> pdb=" O ASP F 164 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ASN F 169 " --> pdb=" O GLU F 165 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG F 170 " --> pdb=" O ALA F 166 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 72 Processing helix chain 'G' and resid 73 through 80 removed outlier: 3.897A pdb=" N ASP G 77 " --> pdb=" O PRO G 74 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N GLY G 78 " --> pdb=" O GLN G 75 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN G 80 " --> pdb=" O ASP G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 116 removed outlier: 3.576A pdb=" N SER G 110 " --> pdb=" O ALA G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 196 Processing helix chain 'I' and resid 39 through 52 Processing helix chain 'I' and resid 75 through 126 removed outlier: 3.671A pdb=" N LYS I 88 " --> pdb=" O VAL I 84 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN I 116 " --> pdb=" O ASP I 112 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU I 126 " --> pdb=" O THR I 122 " (cutoff:3.500A) Processing helix chain 'I' and resid 146 through 155 removed outlier: 4.062A pdb=" N GLY I 150 " --> pdb=" O ASN I 146 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER I 151 " --> pdb=" O ALA I 147 " (cutoff:3.500A) Processing helix chain 'I' and resid 162 through 167 Processing helix chain 'A' and resid 61 through 64 removed outlier: 3.758A pdb=" N LYS A 64 " --> pdb=" O PRO A 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 61 through 64' Processing helix chain 'A' and resid 83 through 87 Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.584A pdb=" N TYR D 32 " --> pdb=" O THR D 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.625A pdb=" N LYS H 64 " --> pdb=" O PRO H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'J' and resid 79 through 83 removed outlier: 4.031A pdb=" N ASP J 83 " --> pdb=" O THR J 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 14 through 15 Processing sheet with id=AA2, first strand: chain 'B' and resid 24 through 26 removed outlier: 3.556A pdb=" N VAL B 26 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE B 34 " --> pdb=" O VAL B 26 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 39 through 41 Processing sheet with id=AA4, first strand: chain 'B' and resid 43 through 44 Processing sheet with id=AA5, first strand: chain 'B' and resid 51 through 52 removed outlier: 5.941A pdb=" N ILE B 51 " --> pdb=" O GLY B 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 58 through 59 removed outlier: 6.571A pdb=" N LEU B 59 " --> pdb=" O VAL B 88 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 120 through 122 removed outlier: 3.603A pdb=" N TYR B 257 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLY B 256 " --> pdb=" O ILE B 179 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ILE B 179 " --> pdb=" O GLY B 256 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG B 229 " --> pdb=" O HIS B 184 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 136 through 140 removed outlier: 3.563A pdb=" N SER B 146 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 151 through 153 Processing sheet with id=AB1, first strand: chain 'B' and resid 164 through 169 removed outlier: 3.586A pdb=" N VAL B 166 " --> pdb=" O ILE B 245 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 303 through 304 removed outlier: 3.820A pdb=" N LYS E 62 " --> pdb=" O GLY B 303 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 16 through 17 Processing sheet with id=AB4, first strand: chain 'C' and resid 24 through 26 removed outlier: 3.501A pdb=" N ILE C 34 " --> pdb=" O VAL C 26 " (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 52 removed outlier: 6.164A pdb=" N ILE C 51 " --> pdb=" O GLY C 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 58 through 59 removed outlier: 7.126A pdb=" N LEU C 59 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N PHE C 87 " --> pdb=" O MET 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 120 through 122 removed outlier: 3.540A pdb=" N ASN C 121 " --> pdb=" O TYR C 257 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR C 257 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N GLY C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N ILE C 179 " --> pdb=" O GLY C 256 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG C 229 " --> pdb=" O HIS C 184 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 151 through 153 Processing sheet with id=AC2, first strand: chain 'C' and resid 164 through 169 removed outlier: 3.510A pdb=" N SER C 247 " --> pdb=" O LEU C 164 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 303 through 304 Processing sheet with id=AC4, first strand: chain 'E' and resid 130 through 132 removed outlier: 3.590A pdb=" N GLU E 131 " --> pdb=" O LYS E 139 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 14 through 17 removed outlier: 3.541A pdb=" N ASN I 28 " --> pdb=" O GLY I 31 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 24 through 25 Processing sheet with id=AC7, first strand: chain 'G' and resid 39 through 41 Processing sheet with id=AC8, first strand: chain 'G' and resid 43 through 44 Processing sheet with id=AC9, first strand: chain 'G' and resid 51 through 52 removed outlier: 6.512A pdb=" N ILE G 51 " --> pdb=" O GLY G 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'G' and resid 58 through 59 removed outlier: 6.412A pdb=" N LEU G 59 " --> pdb=" O VAL G 88 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 100 through 101 removed outlier: 4.015A pdb=" N ILE G 232 " --> pdb=" O ASP G 101 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG G 229 " --> pdb=" O HIS G 184 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ILE G 179 " --> pdb=" O GLY G 256 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N GLY G 256 " --> pdb=" O ILE G 179 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR G 257 " --> pdb=" O ASN G 121 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 100 through 101 removed outlier: 4.015A pdb=" N ILE G 232 " --> pdb=" O ASP G 101 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG G 229 " --> pdb=" O HIS G 184 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 164 through 169 removed outlier: 3.505A pdb=" N VAL G 166 " --> pdb=" O ILE G 245 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 303 through 305 removed outlier: 3.609A pdb=" N LYS I 62 " --> pdb=" O GLY G 303 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N CYS G 305 " --> pdb=" O ASN I 60 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ASN I 60 " --> pdb=" O CYS G 305 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 3 through 7 removed outlier: 3.597A pdb=" N THR A 3 " --> pdb=" O SER A 25 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.577A pdb=" N ALA A 93 " --> pdb=" O GLY A 35B" (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL A 35A" --> pdb=" O HIS A 50 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N HIS A 50 " --> pdb=" O VAL A 35A" (cutoff:3.500A) removed outlier: 7.389A pdb=" N TRP A 36 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR A 58 " --> pdb=" O HIS A 50 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.525A pdb=" N GLY A 100A" --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 4 through 5 removed outlier: 3.503A pdb=" N CYS D 23 " --> pdb=" O ALA D 71 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ALA D 71 " --> pdb=" O CYS D 23 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 9 through 13 removed outlier: 3.674A pdb=" N ALA D 84 " --> pdb=" O VAL D 104 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL D 36 " --> pdb=" O PHE D 87 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 9 through 13 removed outlier: 3.674A pdb=" N ALA D 84 " --> pdb=" O VAL D 104 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.549A pdb=" N THR H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.604A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR H 58 " --> pdb=" O HIS H 50 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 11 through 12 removed outlier: 7.236A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP H 101 " --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY H 100A" --> pdb=" O ASN H 98 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 4 through 5 Processing sheet with id=AE7, first strand: chain 'J' and resid 9 through 13 removed outlier: 3.631A pdb=" N VAL J 104 " --> pdb=" O ALA J 84 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA J 84 " --> pdb=" O VAL J 104 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 9 through 13 removed outlier: 3.631A pdb=" N VAL J 104 " --> pdb=" O ALA J 84 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA J 84 " --> pdb=" O VAL J 104 " (cutoff:3.500A) 553 hydrogen bonds defined for protein. 1482 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: 2.66 Time building geometry restraints manager: 1.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4948 1.34 - 1.46: 3399 1.46 - 1.59: 6376 1.59 - 1.71: 0 1.71 - 1.83: 78 Bond restraints: 14801 Sorted by residual: bond pdb=" CB ASN I 53 " pdb=" CG ASN I 53 " ideal model delta sigma weight residual 1.516 1.557 -0.041 2.50e-02 1.60e+03 2.66e+00 bond pdb=" CB LYS E 143 " pdb=" CG LYS E 143 " ideal model delta sigma weight residual 1.520 1.567 -0.047 3.00e-02 1.11e+03 2.44e+00 bond pdb=" CB ASP B 101 " pdb=" CG ASP B 101 " ideal model delta sigma weight residual 1.516 1.555 -0.039 2.50e-02 1.60e+03 2.44e+00 bond pdb=" C SER C 54 " pdb=" N PRO C 55 " ideal model delta sigma weight residual 1.334 1.368 -0.034 2.34e-02 1.83e+03 2.15e+00 bond pdb=" CB ASN G 322 " pdb=" CG ASN G 322 " ideal model delta sigma weight residual 1.516 1.552 -0.036 2.50e-02 1.60e+03 2.02e+00 ... (remaining 14796 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 19792 2.29 - 4.59: 255 4.59 - 6.88: 42 6.88 - 9.17: 9 9.17 - 11.47: 8 Bond angle restraints: 20106 Sorted by residual: angle pdb=" CA LYS E 143 " pdb=" CB LYS E 143 " pdb=" CG LYS E 143 " ideal model delta sigma weight residual 114.10 123.75 -9.65 2.00e+00 2.50e-01 2.33e+01 angle pdb=" CB MET E 17 " pdb=" CG MET E 17 " pdb=" SD MET E 17 " ideal model delta sigma weight residual 112.70 124.17 -11.47 3.00e+00 1.11e-01 1.46e+01 angle pdb=" C2 NAG N 2 " pdb=" N2 NAG N 2 " pdb=" C7 NAG N 2 " ideal model delta sigma weight residual 124.56 135.89 -11.33 3.00e+00 1.11e-01 1.43e+01 angle pdb=" C2 NAG P 2 " pdb=" N2 NAG P 2 " pdb=" C7 NAG P 2 " ideal model delta sigma weight residual 124.56 135.79 -11.23 3.00e+00 1.11e-01 1.40e+01 angle pdb=" C2 NAG K 2 " pdb=" N2 NAG K 2 " pdb=" C7 NAG K 2 " ideal model delta sigma weight residual 124.56 135.78 -11.22 3.00e+00 1.11e-01 1.40e+01 ... (remaining 20101 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 8275 18.01 - 36.02: 789 36.02 - 54.03: 209 54.03 - 72.04: 52 72.04 - 90.06: 19 Dihedral angle restraints: 9344 sinusoidal: 3758 harmonic: 5586 Sorted by residual: dihedral pdb=" CB CYS G 281 " pdb=" SG CYS G 281 " pdb=" SG CYS G 305 " pdb=" CB CYS G 305 " ideal model delta sinusoidal sigma weight residual 93.00 -178.28 -88.72 1 1.00e+01 1.00e-02 9.39e+01 dihedral pdb=" CB CYS I 144 " pdb=" SG CYS I 144 " pdb=" SG CYS I 148 " pdb=" CB CYS I 148 " ideal model delta sinusoidal sigma weight residual -86.00 -172.52 86.52 1 1.00e+01 1.00e-02 9.02e+01 dihedral pdb=" CB CYS B 281 " pdb=" SG CYS B 281 " pdb=" SG CYS B 305 " pdb=" CB CYS B 305 " ideal model delta sinusoidal sigma weight residual 93.00 169.29 -76.29 1 1.00e+01 1.00e-02 7.32e+01 ... (remaining 9341 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2159 0.093 - 0.187: 187 0.187 - 0.280: 6 0.280 - 0.373: 3 0.373 - 0.467: 2 Chirality restraints: 2357 Sorted by residual: chirality pdb=" C1 NAG E 301 " pdb=" ND2 ASN E 154 " pdb=" C2 NAG E 301 " pdb=" O5 NAG E 301 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.45e+00 chirality pdb=" C1 NAG B 404 " pdb=" ND2 ASN B 38 " pdb=" C2 NAG B 404 " pdb=" O5 NAG B 404 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.72e+00 chirality pdb=" C2 NAG P 2 " pdb=" C1 NAG P 2 " pdb=" C3 NAG P 2 " pdb=" N2 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.19 -0.30 2.00e-01 2.50e+01 2.30e+00 ... (remaining 2354 not shown) Planarity restraints: 2673 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN G 322 " -0.015 2.00e-02 2.50e+03 2.95e-02 8.73e+00 pdb=" C ASN G 322 " 0.051 2.00e-02 2.50e+03 pdb=" O ASN G 322 " -0.019 2.00e-02 2.50e+03 pdb=" N VAL G 323 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL G 323 " -0.045 5.00e-02 4.00e+02 6.78e-02 7.34e+00 pdb=" N PRO G 324 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO G 324 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO G 324 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 323 " 0.043 5.00e-02 4.00e+02 6.49e-02 6.75e+00 pdb=" N PRO C 324 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO C 324 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 324 " 0.035 5.00e-02 4.00e+02 ... (remaining 2670 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3285 2.79 - 3.32: 12719 3.32 - 3.84: 23349 3.84 - 4.37: 24694 4.37 - 4.90: 44413 Nonbonded interactions: 108460 Sorted by model distance: nonbonded pdb=" OE1 GLU E 131 " pdb=" OH TYR E 141 " model vdw 2.260 3.040 nonbonded pdb=" OD1 ASN C 38 " pdb=" OG1 THR C 318 " model vdw 2.261 3.040 nonbonded pdb=" OG1 THR B 65 " pdb=" OE2 GLU B 89 " model vdw 2.261 3.040 nonbonded pdb=" OH TYR G 98 " pdb=" OG SER G 228 " model vdw 2.273 3.040 nonbonded pdb=" O LYS B 27 " pdb=" ND2 ASN E 104 " model vdw 2.289 3.120 ... (remaining 108455 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' selection = (chain 'H' and resid 1 through 112) } ncs_group { reference = (chain 'B' and resid 5 through 405) selection = (chain 'C' and resid 5 through 405) selection = (chain 'G' and (resid 5 through 328 or resid 402 through 406)) } ncs_group { reference = chain 'D' selection = (chain 'J' and resid 1 through 107) } ncs_group { reference = (chain 'E' and resid 3 through 301) selection = (chain 'F' and resid 3 through 301) selection = chain 'I' } ncs_group { reference = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'P' } ncs_group { reference = chain 'L' selection = chain 'O' selection = chain 'Q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.010 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 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 : 0.003 0.050 14859 Z= 0.138 Angle : 0.711 15.786 20259 Z= 0.362 Chirality : 0.050 0.467 2357 Planarity : 0.004 0.068 2646 Dihedral : 15.597 90.056 5693 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.79 % Favored : 94.00 % Rotamer: Outliers : 2.69 % Allowed : 21.91 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -1.44 (0.18), residues: 1934 helix: -0.54 (0.25), residues: 333 sheet: 0.41 (0.26), residues: 421 loop : -1.68 (0.17), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 150 TYR 0.033 0.001 TYR C 302 PHE 0.018 0.001 PHE G 159 TRP 0.022 0.001 TRP B 127 HIS 0.016 0.001 HIS I 26 Details of bonding type rmsd covalent geometry : bond 0.00279 (14801) covalent geometry : angle 0.67981 (20106) SS BOND : bond 0.00283 ( 21) SS BOND : angle 0.99407 ( 42) hydrogen bonds : bond 0.26941 ( 522) hydrogen bonds : angle 9.15327 ( 1482) link_BETA1-4 : bond 0.00411 ( 10) link_BETA1-4 : angle 1.74377 ( 30) link_NAG-ASN : bond 0.00784 ( 27) link_NAG-ASN : angle 3.18216 ( 81) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 33 time to evaluate : 0.551 Fit side-chains REVERT: B 320 MET cc_start: 0.8323 (ppp) cc_final: 0.7642 (ppp) REVERT: C 142 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7721 (ttp80) REVERT: C 320 MET cc_start: 0.7666 (ptt) cc_final: 0.7031 (ptt) REVERT: F 115 MET cc_start: 0.8706 (ppp) cc_final: 0.8479 (ppp) REVERT: F 141 TYR cc_start: 0.3969 (OUTLIER) cc_final: 0.2328 (m-80) outliers start: 35 outliers final: 17 residues processed: 67 average time/residue: 0.0923 time to fit residues: 10.4004 Evaluate side-chains 46 residues out of total 1681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 27 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 CYS Chi-restraints excluded: chain B residue 52 CYS Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 142 ARG Chi-restraints excluded: chain C residue 268 MET Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 137 CYS Chi-restraints excluded: chain F residue 141 TYR Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain G residue 175 ASP Chi-restraints excluded: chain G residue 193 PHE Chi-restraints excluded: chain G residue 260 ILE Chi-restraints excluded: chain G residue 328 THR Chi-restraints excluded: chain I residue 6 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 40.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 158 ASN B 216 ASN C 80 GLN C 81 ASN C 121 ASN C 145 ASN C 171 ASN ** C 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 ASN ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 HIS ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 12 ASN F 42 GLN F 106 HIS F 172 GLN G 6 ASN G 17 HIS G 144 ASN G 322 ASN I 12 ASN I 49 ASN I 78 GLN I 172 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.043728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.031753 restraints weight = 122937.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.032511 restraints weight = 68936.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.033003 restraints weight = 45911.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.033327 restraints weight = 34335.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.033601 restraints weight = 27724.690| |-----------------------------------------------------------------------------| r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.074 14859 Z= 0.425 Angle : 0.887 14.644 20259 Z= 0.445 Chirality : 0.053 0.373 2357 Planarity : 0.006 0.070 2646 Dihedral : 8.027 59.682 2875 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.96 % Favored : 91.83 % Rotamer: Outliers : 6.76 % Allowed : 18.29 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -1.13 (0.18), residues: 1934 helix: 0.92 (0.26), residues: 348 sheet: -0.06 (0.23), residues: 468 loop : -1.68 (0.18), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 307 TYR 0.024 0.003 TYR B 195 PHE 0.032 0.003 PHE C 258 TRP 0.013 0.002 TRP C 84 HIS 0.009 0.003 HIS E 106 Details of bonding type rmsd covalent geometry : bond 0.00912 (14801) covalent geometry : angle 0.85933 (20106) SS BOND : bond 0.00864 ( 21) SS BOND : angle 1.84310 ( 42) hydrogen bonds : bond 0.05526 ( 522) hydrogen bonds : angle 6.06750 ( 1482) link_BETA1-4 : bond 0.00480 ( 10) link_BETA1-4 : angle 2.14031 ( 30) link_NAG-ASN : bond 0.00634 ( 27) link_NAG-ASN : angle 3.17629 ( 81) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 27 time to evaluate : 0.616 Fit side-chains REVERT: B 75 GLN cc_start: 0.9047 (OUTLIER) cc_final: 0.8290 (pm20) REVERT: B 320 MET cc_start: 0.8566 (ppp) cc_final: 0.8294 (ppp) REVERT: C 68 ASP cc_start: 0.8957 (OUTLIER) cc_final: 0.8638 (t0) REVERT: C 119 GLU cc_start: 0.8957 (OUTLIER) cc_final: 0.8637 (mp0) REVERT: C 320 MET cc_start: 0.8154 (ptt) cc_final: 0.7437 (ptt) REVERT: E 167 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7689 (mm) REVERT: F 62 LYS cc_start: 0.9006 (OUTLIER) cc_final: 0.8432 (mmmt) REVERT: F 115 MET cc_start: 0.8855 (ppp) cc_final: 0.8546 (ppp) REVERT: F 141 TYR cc_start: 0.4511 (OUTLIER) cc_final: 0.2601 (m-80) REVERT: I 17 MET cc_start: 0.4226 (OUTLIER) cc_final: 0.3730 (ptt) outliers start: 88 outliers final: 42 residues processed: 112 average time/residue: 0.0990 time to fit residues: 18.0280 Evaluate side-chains 75 residues out of total 1681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 26 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 CYS Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 52 CYS Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain C residue 30 CYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 142 ARG Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 268 MET Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 137 CYS Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain F residue 62 LYS Chi-restraints excluded: chain F residue 141 TYR Chi-restraints excluded: chain F residue 162 TYR Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 168 ASN Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 52 CYS Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 171 ASN Chi-restraints excluded: chain G residue 193 PHE Chi-restraints excluded: chain G residue 260 ILE Chi-restraints excluded: chain G residue 328 THR Chi-restraints excluded: chain I residue 17 MET Chi-restraints excluded: chain I residue 115 MET Chi-restraints excluded: chain I residue 144 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 158 optimal weight: 40.0000 chunk 176 optimal weight: 40.0000 chunk 86 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 chunk 187 optimal weight: 40.0000 chunk 180 optimal weight: 40.0000 chunk 4 optimal weight: 0.9980 chunk 79 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 GLN ** C 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 144 ASN G 250 ASN G 322 ASN I 12 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.044804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.032800 restraints weight = 120516.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.033600 restraints weight = 66469.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.034136 restraints weight = 43510.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.034508 restraints weight = 31991.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.034779 restraints weight = 25313.871| |-----------------------------------------------------------------------------| r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14859 Z= 0.146 Angle : 0.637 14.211 20259 Z= 0.316 Chirality : 0.048 0.354 2357 Planarity : 0.004 0.069 2646 Dihedral : 7.426 58.854 2869 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.15 % Favored : 93.64 % Rotamer: Outliers : 4.00 % Allowed : 21.29 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % 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 aren not related in a simple way. whole: -0.82 (0.19), residues: 1934 helix: 1.51 (0.27), residues: 348 sheet: 0.06 (0.24), residues: 458 loop : -1.54 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 307 TYR 0.012 0.001 TYR B 195 PHE 0.013 0.001 PHE I 9 TRP 0.009 0.001 TRP I 14 HIS 0.007 0.001 HIS I 26 Details of bonding type rmsd covalent geometry : bond 0.00319 (14801) covalent geometry : angle 0.60726 (20106) SS BOND : bond 0.00517 ( 21) SS BOND : angle 1.26256 ( 42) hydrogen bonds : bond 0.04554 ( 522) hydrogen bonds : angle 5.30944 ( 1482) link_BETA1-4 : bond 0.00406 ( 10) link_BETA1-4 : angle 1.80715 ( 30) link_NAG-ASN : bond 0.00503 ( 27) link_NAG-ASN : angle 2.82274 ( 81) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 26 time to evaluate : 0.570 Fit side-chains revert: symmetry clash REVERT: B 320 MET cc_start: 0.8535 (ppp) cc_final: 0.7483 (ppp) REVERT: C 119 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8400 (mp0) REVERT: C 320 MET cc_start: 0.8092 (ptt) cc_final: 0.7307 (ptt) REVERT: E 12 ASN cc_start: 0.8908 (OUTLIER) cc_final: 0.8619 (m-40) REVERT: E 167 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7759 (mm) REVERT: F 62 LYS cc_start: 0.9035 (OUTLIER) cc_final: 0.8499 (mmmt) REVERT: F 115 MET cc_start: 0.8785 (ppp) cc_final: 0.8095 (ppp) REVERT: F 141 TYR cc_start: 0.4153 (OUTLIER) cc_final: 0.2211 (m-80) REVERT: G 104 ASP cc_start: 0.8378 (OUTLIER) cc_final: 0.8025 (t0) outliers start: 52 outliers final: 33 residues processed: 76 average time/residue: 0.0977 time to fit residues: 12.5660 Evaluate side-chains 65 residues out of total 1681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 26 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 CYS Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 52 CYS Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain C residue 30 CYS Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 142 ARG Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 268 MET Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain E residue 12 ASN Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 137 CYS Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain F residue 62 LYS Chi-restraints excluded: chain F residue 141 TYR Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 52 CYS Chi-restraints excluded: chain G residue 104 ASP Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 171 ASN Chi-restraints excluded: chain G residue 193 PHE Chi-restraints excluded: chain G residue 260 ILE Chi-restraints excluded: chain G residue 277 CYS Chi-restraints excluded: chain G residue 281 CYS Chi-restraints excluded: chain I residue 115 MET Chi-restraints excluded: chain I residue 144 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 140 optimal weight: 7.9990 chunk 150 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 121 optimal weight: 0.4980 chunk 29 optimal weight: 1.9990 chunk 185 optimal weight: 50.0000 chunk 110 optimal weight: 0.9990 chunk 56 optimal weight: 8.9990 chunk 129 optimal weight: 4.9990 chunk 120 optimal weight: 0.6980 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 216 ASN ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 144 ASN G 322 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.044651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.032662 restraints weight = 120496.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.033490 restraints weight = 65373.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.034036 restraints weight = 42185.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.034385 restraints weight = 30712.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.034668 restraints weight = 24501.744| |-----------------------------------------------------------------------------| r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14859 Z= 0.158 Angle : 0.609 13.827 20259 Z= 0.301 Chirality : 0.047 0.332 2357 Planarity : 0.004 0.070 2646 Dihedral : 7.104 59.669 2867 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.93 % Favored : 92.86 % Rotamer: Outliers : 4.30 % Allowed : 21.60 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % 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 aren not related in a simple way. whole: -0.68 (0.19), residues: 1934 helix: 1.86 (0.27), residues: 353 sheet: 0.14 (0.24), residues: 461 loop : -1.55 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 90 TYR 0.011 0.001 TYR B 195 PHE 0.017 0.001 PHE F 9 TRP 0.009 0.001 TRP I 14 HIS 0.006 0.001 HIS I 26 Details of bonding type rmsd covalent geometry : bond 0.00347 (14801) covalent geometry : angle 0.57928 (20106) SS BOND : bond 0.00434 ( 21) SS BOND : angle 1.18842 ( 42) hydrogen bonds : bond 0.04051 ( 522) hydrogen bonds : angle 4.87727 ( 1482) link_BETA1-4 : bond 0.00330 ( 10) link_BETA1-4 : angle 1.71671 ( 30) link_NAG-ASN : bond 0.00487 ( 27) link_NAG-ASN : angle 2.75746 ( 81) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 26 time to evaluate : 0.484 Fit side-chains revert: symmetry clash REVERT: B 75 GLN cc_start: 0.8998 (OUTLIER) cc_final: 0.8202 (pm20) REVERT: B 320 MET cc_start: 0.8531 (ppp) cc_final: 0.7305 (ppp) REVERT: C 68 ASP cc_start: 0.8932 (OUTLIER) cc_final: 0.8578 (t0) REVERT: C 119 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8521 (mp0) REVERT: C 320 MET cc_start: 0.7955 (ptt) cc_final: 0.7194 (ptt) REVERT: E 12 ASN cc_start: 0.8930 (OUTLIER) cc_final: 0.8511 (m-40) REVERT: F 62 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8487 (mmmt) REVERT: F 115 MET cc_start: 0.8762 (ppp) cc_final: 0.8186 (ppp) REVERT: F 141 TYR cc_start: 0.4194 (OUTLIER) cc_final: 0.2341 (m-80) REVERT: G 104 ASP cc_start: 0.8384 (OUTLIER) cc_final: 0.8142 (t0) REVERT: I 116 ASN cc_start: 0.9376 (OUTLIER) cc_final: 0.9149 (m-40) outliers start: 56 outliers final: 33 residues processed: 80 average time/residue: 0.0993 time to fit residues: 13.0698 Evaluate side-chains 67 residues out of total 1681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 26 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain C residue 30 CYS Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 142 ARG Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 216 ASN Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 266 SER Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain E residue 12 ASN Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 62 LYS Chi-restraints excluded: chain F residue 141 TYR Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 52 CYS Chi-restraints excluded: chain G residue 104 ASP Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 193 PHE Chi-restraints excluded: chain G residue 260 ILE Chi-restraints excluded: chain G residue 277 CYS Chi-restraints excluded: chain G residue 281 CYS Chi-restraints excluded: chain G residue 328 THR Chi-restraints excluded: chain I residue 115 MET Chi-restraints excluded: chain I residue 116 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 175 optimal weight: 50.0000 chunk 53 optimal weight: 0.0060 chunk 142 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 37 optimal weight: 7.9990 chunk 192 optimal weight: 50.0000 chunk 90 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 161 optimal weight: 0.9990 chunk 176 optimal weight: 30.0000 chunk 150 optimal weight: 5.9990 overall best weight: 3.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 169 ASN G 322 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.043585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.031915 restraints weight = 121622.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.032691 restraints weight = 67205.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.033166 restraints weight = 43954.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.033535 restraints weight = 32640.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.033769 restraints weight = 26058.532| |-----------------------------------------------------------------------------| r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 14859 Z= 0.271 Angle : 0.703 13.684 20259 Z= 0.346 Chirality : 0.048 0.332 2357 Planarity : 0.004 0.072 2646 Dihedral : 7.408 58.341 2861 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.81 % Favored : 91.99 % Rotamer: Outliers : 5.15 % Allowed : 21.60 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % 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 aren not related in a simple way. whole: -0.79 (0.19), residues: 1934 helix: 1.64 (0.27), residues: 357 sheet: 0.13 (0.24), residues: 454 loop : -1.62 (0.18), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 222 TYR 0.016 0.002 TYR B 195 PHE 0.019 0.002 PHE C 258 TRP 0.006 0.001 TRP C 84 HIS 0.007 0.002 HIS E 106 Details of bonding type rmsd covalent geometry : bond 0.00594 (14801) covalent geometry : angle 0.67451 (20106) SS BOND : bond 0.00614 ( 21) SS BOND : angle 1.41859 ( 42) hydrogen bonds : bond 0.04274 ( 522) hydrogen bonds : angle 5.09940 ( 1482) link_BETA1-4 : bond 0.00359 ( 10) link_BETA1-4 : angle 1.87564 ( 30) link_NAG-ASN : bond 0.00482 ( 27) link_NAG-ASN : angle 2.91167 ( 81) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 26 time to evaluate : 0.588 Fit side-chains revert: symmetry clash REVERT: B 75 GLN cc_start: 0.9091 (OUTLIER) cc_final: 0.8299 (pm20) REVERT: B 222 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.8093 (mmm160) REVERT: B 320 MET cc_start: 0.8558 (ppp) cc_final: 0.7238 (ppp) REVERT: C 68 ASP cc_start: 0.8979 (OUTLIER) cc_final: 0.8774 (t0) REVERT: C 119 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8484 (mp0) REVERT: C 320 MET cc_start: 0.7981 (ptt) cc_final: 0.7171 (ptt) REVERT: E 12 ASN cc_start: 0.8990 (OUTLIER) cc_final: 0.8726 (m-40) REVERT: F 62 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8475 (mmmt) REVERT: F 115 MET cc_start: 0.8800 (ppp) cc_final: 0.8263 (ppp) REVERT: F 141 TYR cc_start: 0.4384 (OUTLIER) cc_final: 0.2600 (m-80) REVERT: I 51 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8494 (mptt) REVERT: I 116 ASN cc_start: 0.9473 (OUTLIER) cc_final: 0.9215 (m-40) outliers start: 67 outliers final: 41 residues processed: 91 average time/residue: 0.0976 time to fit residues: 14.7308 Evaluate side-chains 76 residues out of total 1681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 26 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain C residue 30 CYS Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 142 ARG Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 266 SER Chi-restraints excluded: chain C residue 268 MET Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain E residue 12 ASN Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 62 LYS Chi-restraints excluded: chain F residue 141 TYR Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain G residue 18 HIS Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 52 CYS Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 171 ASN Chi-restraints excluded: chain G residue 193 PHE Chi-restraints excluded: chain G residue 260 ILE Chi-restraints excluded: chain G residue 281 CYS Chi-restraints excluded: chain G residue 328 THR Chi-restraints excluded: chain I residue 51 LYS Chi-restraints excluded: chain I residue 115 MET Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain I residue 144 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 149 optimal weight: 50.0000 chunk 37 optimal weight: 0.9990 chunk 143 optimal weight: 6.9990 chunk 111 optimal weight: 8.9990 chunk 165 optimal weight: 50.0000 chunk 13 optimal weight: 10.0000 chunk 132 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 181 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 192 optimal weight: 50.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 HIS ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 125 GLN ** G 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 34 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.042958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.031429 restraints weight = 119788.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.032179 restraints weight = 65693.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.032690 restraints weight = 42823.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.033016 restraints weight = 31502.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.033287 restraints weight = 25170.303| |-----------------------------------------------------------------------------| r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 14859 Z= 0.290 Angle : 0.737 13.473 20259 Z= 0.365 Chirality : 0.049 0.346 2357 Planarity : 0.004 0.071 2646 Dihedral : 7.780 57.623 2861 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.27 % Favored : 91.52 % Rotamer: Outliers : 5.46 % Allowed : 21.75 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % 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 aren not related in a simple way. whole: -1.01 (0.19), residues: 1934 helix: 1.43 (0.26), residues: 355 sheet: -0.09 (0.25), residues: 449 loop : -1.69 (0.18), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 201 TYR 0.016 0.002 TYR G 94 PHE 0.022 0.002 PHE C 258 TRP 0.007 0.001 TRP F 21 HIS 0.007 0.002 HIS E 106 Details of bonding type rmsd covalent geometry : bond 0.00634 (14801) covalent geometry : angle 0.70562 (20106) SS BOND : bond 0.00668 ( 21) SS BOND : angle 1.76976 ( 42) hydrogen bonds : bond 0.04405 ( 522) hydrogen bonds : angle 5.29116 ( 1482) link_BETA1-4 : bond 0.00328 ( 10) link_BETA1-4 : angle 1.93765 ( 30) link_NAG-ASN : bond 0.00484 ( 27) link_NAG-ASN : angle 3.01226 ( 81) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 26 time to evaluate : 0.496 Fit side-chains revert: symmetry clash REVERT: B 75 GLN cc_start: 0.9164 (OUTLIER) cc_final: 0.8299 (pm20) REVERT: B 82 LYS cc_start: 0.9231 (OUTLIER) cc_final: 0.9007 (mttp) REVERT: B 222 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.8166 (mmm160) REVERT: B 320 MET cc_start: 0.8520 (ppp) cc_final: 0.7380 (ppp) REVERT: C 68 ASP cc_start: 0.9031 (OUTLIER) cc_final: 0.8717 (t0) REVERT: C 117 THR cc_start: 0.8760 (OUTLIER) cc_final: 0.8092 (m) REVERT: C 119 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8473 (mp0) REVERT: C 168 MET cc_start: 0.8525 (tmm) cc_final: 0.8268 (tmm) REVERT: F 9 PHE cc_start: 0.8081 (t80) cc_final: 0.7649 (t80) REVERT: F 62 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8449 (mmmt) REVERT: F 115 MET cc_start: 0.8537 (ppp) cc_final: 0.7854 (ppp) REVERT: F 141 TYR cc_start: 0.4863 (OUTLIER) cc_final: 0.3438 (m-80) REVERT: G 104 ASP cc_start: 0.8153 (OUTLIER) cc_final: 0.7915 (t70) REVERT: I 17 MET cc_start: 0.5361 (ppp) cc_final: 0.4917 (ppp) REVERT: I 51 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.7556 (mptt) REVERT: I 116 ASN cc_start: 0.9523 (OUTLIER) cc_final: 0.9318 (m-40) outliers start: 71 outliers final: 40 residues processed: 96 average time/residue: 0.1067 time to fit residues: 16.3042 Evaluate side-chains 77 residues out of total 1681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 26 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain C residue 30 CYS Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 142 ARG Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 266 SER Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 62 LYS Chi-restraints excluded: chain F residue 141 TYR Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 52 CYS Chi-restraints excluded: chain G residue 104 ASP Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 171 ASN Chi-restraints excluded: chain G residue 193 PHE Chi-restraints excluded: chain G residue 260 ILE Chi-restraints excluded: chain G residue 281 CYS Chi-restraints excluded: chain G residue 328 THR Chi-restraints excluded: chain I residue 51 LYS Chi-restraints excluded: chain I residue 115 MET Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain I residue 144 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 159 optimal weight: 5.9990 chunk 130 optimal weight: 8.9990 chunk 38 optimal weight: 0.6980 chunk 163 optimal weight: 50.0000 chunk 12 optimal weight: 2.9990 chunk 150 optimal weight: 9.9990 chunk 16 optimal weight: 0.9980 chunk 114 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 162 optimal weight: 50.0000 chunk 17 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 159 HIS G 322 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.043642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.031994 restraints weight = 119263.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.032772 restraints weight = 65631.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.033254 restraints weight = 42717.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.033619 restraints weight = 31666.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.033865 restraints weight = 25302.620| |-----------------------------------------------------------------------------| r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14859 Z= 0.164 Angle : 0.640 13.517 20259 Z= 0.314 Chirality : 0.048 0.344 2357 Planarity : 0.004 0.070 2646 Dihedral : 7.275 59.124 2858 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.14 % Favored : 92.66 % Rotamer: Outliers : 3.92 % Allowed : 23.44 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % 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 aren not related in a simple way. whole: -0.81 (0.19), residues: 1934 helix: 1.64 (0.26), residues: 356 sheet: 0.03 (0.25), residues: 434 loop : -1.57 (0.18), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 222 TYR 0.014 0.001 TYR F 162 PHE 0.017 0.001 PHE I 9 TRP 0.007 0.001 TRP G 127 HIS 0.005 0.001 HIS E 26 Details of bonding type rmsd covalent geometry : bond 0.00363 (14801) covalent geometry : angle 0.60998 (20106) SS BOND : bond 0.00430 ( 21) SS BOND : angle 1.30633 ( 42) hydrogen bonds : bond 0.03982 ( 522) hydrogen bonds : angle 4.91682 ( 1482) link_BETA1-4 : bond 0.00316 ( 10) link_BETA1-4 : angle 1.79445 ( 30) link_NAG-ASN : bond 0.00483 ( 27) link_NAG-ASN : angle 2.85480 ( 81) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 26 time to evaluate : 0.597 Fit side-chains revert: symmetry clash REVERT: B 75 GLN cc_start: 0.9056 (OUTLIER) cc_final: 0.8218 (pm20) REVERT: B 82 LYS cc_start: 0.9208 (OUTLIER) cc_final: 0.8961 (mttp) REVERT: B 222 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.8074 (mmm160) REVERT: B 320 MET cc_start: 0.8430 (ppp) cc_final: 0.7280 (ppp) REVERT: C 68 ASP cc_start: 0.9053 (OUTLIER) cc_final: 0.8690 (t0) REVERT: C 119 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8489 (mp0) REVERT: F 9 PHE cc_start: 0.8137 (t80) cc_final: 0.7721 (t80) REVERT: F 62 LYS cc_start: 0.9022 (OUTLIER) cc_final: 0.8486 (mmmt) REVERT: F 115 MET cc_start: 0.8668 (ppp) cc_final: 0.7893 (ppp) REVERT: I 51 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8518 (mttm) REVERT: I 116 ASN cc_start: 0.9516 (OUTLIER) cc_final: 0.9289 (m-40) outliers start: 51 outliers final: 36 residues processed: 76 average time/residue: 0.1047 time to fit residues: 12.9726 Evaluate side-chains 70 residues out of total 1681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 26 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain C residue 30 CYS Chi-restraints excluded: chain C residue 64 CYS Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 142 ARG Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 266 SER Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 62 LYS Chi-restraints excluded: chain F residue 162 TYR Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 52 CYS Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 193 PHE Chi-restraints excluded: chain G residue 260 ILE Chi-restraints excluded: chain G residue 281 CYS Chi-restraints excluded: chain G residue 328 THR Chi-restraints excluded: chain I residue 51 LYS Chi-restraints excluded: chain I residue 115 MET Chi-restraints excluded: chain I residue 116 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 69 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 82 optimal weight: 8.9990 chunk 109 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 chunk 100 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 169 ASN G 322 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.043650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.032212 restraints weight = 115500.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.033008 restraints weight = 61273.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.033545 restraints weight = 39519.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.033890 restraints weight = 28522.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.034170 restraints weight = 22471.970| |-----------------------------------------------------------------------------| r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14859 Z= 0.165 Angle : 0.638 13.429 20259 Z= 0.312 Chirality : 0.047 0.339 2357 Planarity : 0.004 0.070 2646 Dihedral : 7.060 58.539 2856 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.98 % Favored : 92.86 % Rotamer: Outliers : 4.23 % Allowed : 22.98 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % 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 aren not related in a simple way. whole: -0.73 (0.19), residues: 1934 helix: 1.81 (0.27), residues: 358 sheet: 0.05 (0.25), residues: 434 loop : -1.53 (0.18), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 222 TYR 0.013 0.001 TYR F 162 PHE 0.015 0.001 PHE I 9 TRP 0.006 0.001 TRP I 92 HIS 0.005 0.001 HIS E 26 Details of bonding type rmsd covalent geometry : bond 0.00366 (14801) covalent geometry : angle 0.60865 (20106) SS BOND : bond 0.00441 ( 21) SS BOND : angle 1.28696 ( 42) hydrogen bonds : bond 0.03872 ( 522) hydrogen bonds : angle 4.74684 ( 1482) link_BETA1-4 : bond 0.00312 ( 10) link_BETA1-4 : angle 1.77752 ( 30) link_NAG-ASN : bond 0.00483 ( 27) link_NAG-ASN : angle 2.82499 ( 81) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 26 time to evaluate : 0.563 Fit side-chains revert: symmetry clash REVERT: B 75 GLN cc_start: 0.9036 (OUTLIER) cc_final: 0.8206 (pm20) REVERT: B 82 LYS cc_start: 0.9192 (OUTLIER) cc_final: 0.8969 (mttp) REVERT: B 222 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.8109 (mmm160) REVERT: B 320 MET cc_start: 0.8470 (ppp) cc_final: 0.7325 (ppp) REVERT: C 68 ASP cc_start: 0.8976 (OUTLIER) cc_final: 0.8635 (t0) REVERT: C 320 MET cc_start: 0.8239 (ptt) cc_final: 0.7707 (ptt) REVERT: F 9 PHE cc_start: 0.7879 (t80) cc_final: 0.7512 (t80) REVERT: F 62 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8508 (mmmt) REVERT: F 115 MET cc_start: 0.8571 (ppp) cc_final: 0.7708 (ppp) REVERT: I 17 MET cc_start: 0.5838 (ppp) cc_final: 0.5260 (ppp) REVERT: I 116 ASN cc_start: 0.9490 (OUTLIER) cc_final: 0.9246 (m-40) outliers start: 55 outliers final: 40 residues processed: 80 average time/residue: 0.1020 time to fit residues: 13.3820 Evaluate side-chains 72 residues out of total 1681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 26 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain C residue 30 CYS Chi-restraints excluded: chain C residue 64 CYS Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 142 ARG Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 266 SER Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 62 LYS Chi-restraints excluded: chain F residue 162 TYR Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 52 CYS Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 171 ASN Chi-restraints excluded: chain G residue 193 PHE Chi-restraints excluded: chain G residue 260 ILE Chi-restraints excluded: chain G residue 277 CYS Chi-restraints excluded: chain G residue 281 CYS Chi-restraints excluded: chain G residue 328 THR Chi-restraints excluded: chain I residue 115 MET Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain I residue 144 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 46 optimal weight: 4.9990 chunk 66 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 84 optimal weight: 20.0000 chunk 185 optimal weight: 50.0000 chunk 6 optimal weight: 5.9990 chunk 154 optimal weight: 30.0000 chunk 86 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 322 ASN I 116 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.042953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.031437 restraints weight = 118520.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.032208 restraints weight = 63877.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.032733 restraints weight = 41318.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.033062 restraints weight = 30089.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.033334 restraints weight = 23968.764| |-----------------------------------------------------------------------------| r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 14859 Z= 0.307 Angle : 0.760 13.195 20259 Z= 0.375 Chirality : 0.050 0.342 2357 Planarity : 0.004 0.072 2646 Dihedral : 7.655 59.535 2856 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.27 % Favored : 91.47 % Rotamer: Outliers : 4.38 % Allowed : 22.98 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % 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 aren not related in a simple way. whole: -0.97 (0.19), residues: 1934 helix: 1.51 (0.26), residues: 355 sheet: -0.19 (0.25), residues: 451 loop : -1.63 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 261 TYR 0.016 0.002 TYR B 195 PHE 0.027 0.002 PHE I 9 TRP 0.007 0.001 TRP E 21 HIS 0.006 0.002 HIS G 17 Details of bonding type rmsd covalent geometry : bond 0.00671 (14801) covalent geometry : angle 0.73078 (20106) SS BOND : bond 0.00747 ( 21) SS BOND : angle 1.79402 ( 42) hydrogen bonds : bond 0.04359 ( 522) hydrogen bonds : angle 5.20187 ( 1482) link_BETA1-4 : bond 0.00334 ( 10) link_BETA1-4 : angle 2.00621 ( 30) link_NAG-ASN : bond 0.00502 ( 27) link_NAG-ASN : angle 2.98685 ( 81) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 27 time to evaluate : 0.564 Fit side-chains revert: symmetry clash REVERT: B 75 GLN cc_start: 0.9149 (OUTLIER) cc_final: 0.8290 (pm20) REVERT: B 82 LYS cc_start: 0.9216 (OUTLIER) cc_final: 0.8990 (mttp) REVERT: B 222 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.8143 (mmm-85) REVERT: B 226 ILE cc_start: 0.8898 (OUTLIER) cc_final: 0.8474 (mm) REVERT: B 320 MET cc_start: 0.8477 (ppp) cc_final: 0.7380 (ppp) REVERT: C 68 ASP cc_start: 0.8975 (OUTLIER) cc_final: 0.8672 (t0) REVERT: C 320 MET cc_start: 0.8321 (ptt) cc_final: 0.7740 (ptt) REVERT: F 9 PHE cc_start: 0.8129 (t80) cc_final: 0.7704 (t80) REVERT: F 62 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8451 (mmmt) REVERT: F 115 MET cc_start: 0.8608 (ppp) cc_final: 0.7817 (ppp) REVERT: F 141 TYR cc_start: 0.5038 (OUTLIER) cc_final: 0.4003 (m-80) REVERT: G 268 MET cc_start: 0.9106 (OUTLIER) cc_final: 0.8233 (ttp) outliers start: 57 outliers final: 40 residues processed: 82 average time/residue: 0.1014 time to fit residues: 13.6138 Evaluate side-chains 74 residues out of total 1681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 26 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain C residue 30 CYS Chi-restraints excluded: chain C residue 64 CYS Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 142 ARG Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 266 SER Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 62 LYS Chi-restraints excluded: chain F residue 141 TYR Chi-restraints excluded: chain F residue 162 TYR Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 52 CYS Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 171 ASN Chi-restraints excluded: chain G residue 193 PHE Chi-restraints excluded: chain G residue 260 ILE Chi-restraints excluded: chain G residue 268 MET Chi-restraints excluded: chain G residue 281 CYS Chi-restraints excluded: chain G residue 328 THR Chi-restraints excluded: chain I residue 6 ILE Chi-restraints excluded: chain I residue 115 MET Chi-restraints excluded: chain I residue 144 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 16 optimal weight: 3.9990 chunk 144 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 81 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 59 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 87 optimal weight: 0.3980 chunk 5 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 81 ASN ** E 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 ASN G 322 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.043890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.032407 restraints weight = 115375.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.033225 restraints weight = 61211.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.033738 restraints weight = 39108.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.034120 restraints weight = 28292.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.034372 restraints weight = 22208.600| |-----------------------------------------------------------------------------| r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.108 14859 Z= 0.129 Angle : 0.652 13.485 20259 Z= 0.318 Chirality : 0.048 0.338 2357 Planarity : 0.004 0.070 2646 Dihedral : 7.021 59.565 2856 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.26 % Favored : 93.49 % Rotamer: Outliers : 3.07 % Allowed : 23.98 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % 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 aren not related in a simple way. whole: -0.73 (0.19), residues: 1934 helix: 1.85 (0.27), residues: 358 sheet: -0.02 (0.25), residues: 434 loop : -1.52 (0.18), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 222 TYR 0.014 0.001 TYR F 162 PHE 0.028 0.001 PHE I 9 TRP 0.008 0.001 TRP G 127 HIS 0.005 0.001 HIS I 26 Details of bonding type rmsd covalent geometry : bond 0.00293 (14801) covalent geometry : angle 0.61998 (20106) SS BOND : bond 0.00459 ( 21) SS BOND : angle 1.87649 ( 42) hydrogen bonds : bond 0.03816 ( 522) hydrogen bonds : angle 4.68825 ( 1482) link_BETA1-4 : bond 0.00342 ( 10) link_BETA1-4 : angle 1.77450 ( 30) link_NAG-ASN : bond 0.00500 ( 27) link_NAG-ASN : angle 2.80800 ( 81) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 26 time to evaluate : 0.571 Fit side-chains revert: symmetry clash REVERT: B 82 LYS cc_start: 0.9192 (OUTLIER) cc_final: 0.8951 (mttp) REVERT: B 320 MET cc_start: 0.8466 (ppp) cc_final: 0.7304 (ppp) REVERT: C 320 MET cc_start: 0.8207 (ptt) cc_final: 0.7609 (ptt) REVERT: F 9 PHE cc_start: 0.7969 (t80) cc_final: 0.7645 (t80) REVERT: F 62 LYS cc_start: 0.9024 (OUTLIER) cc_final: 0.8555 (mmmt) REVERT: F 115 MET cc_start: 0.8552 (ppp) cc_final: 0.7603 (ppp) outliers start: 40 outliers final: 32 residues processed: 65 average time/residue: 0.1047 time to fit residues: 11.2516 Evaluate side-chains 60 residues out of total 1681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 26 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain C residue 30 CYS Chi-restraints excluded: chain C residue 64 CYS Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 142 ARG Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 266 SER Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 62 LYS Chi-restraints excluded: chain F residue 162 TYR Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 52 CYS Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 260 ILE Chi-restraints excluded: chain G residue 281 CYS Chi-restraints excluded: chain G residue 328 THR Chi-restraints excluded: chain I residue 115 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 107 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 190 optimal weight: 40.0000 chunk 79 optimal weight: 9.9990 chunk 131 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 144 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 183 optimal weight: 0.0870 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 322 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.043912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.032383 restraints weight = 115266.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.033196 restraints weight = 61292.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.033747 restraints weight = 39258.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.034084 restraints weight = 28281.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.034350 restraints weight = 22325.800| |-----------------------------------------------------------------------------| r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.173 14859 Z= 0.183 Angle : 0.841 59.200 20259 Z= 0.466 Chirality : 0.048 0.477 2357 Planarity : 0.004 0.070 2646 Dihedral : 6.978 59.555 2854 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.36 % Favored : 93.38 % Rotamer: Outliers : 2.92 % Allowed : 24.14 % Favored : 72.94 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % 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 aren not related in a simple way. whole: -0.72 (0.19), residues: 1934 helix: 1.86 (0.27), residues: 358 sheet: -0.01 (0.25), residues: 434 loop : -1.52 (0.18), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 222 TYR 0.014 0.001 TYR F 162 PHE 0.025 0.001 PHE I 9 TRP 0.008 0.001 TRP G 127 HIS 0.005 0.001 HIS E 26 Details of bonding type rmsd covalent geometry : bond 0.00363 (14801) covalent geometry : angle 0.81809 (20106) SS BOND : bond 0.00483 ( 21) SS BOND : angle 1.85351 ( 42) hydrogen bonds : bond 0.03814 ( 522) hydrogen bonds : angle 4.68423 ( 1482) link_BETA1-4 : bond 0.00560 ( 10) link_BETA1-4 : angle 1.86445 ( 30) link_NAG-ASN : bond 0.00501 ( 27) link_NAG-ASN : angle 2.80651 ( 81) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2133.24 seconds wall clock time: 38 minutes 9.51 seconds (2289.51 seconds total)