Starting phenix.real_space_refine on Tue Nov 19 13:18:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ja0_61286/11_2024/9ja0_61286.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ja0_61286/11_2024/9ja0_61286.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ja0_61286/11_2024/9ja0_61286.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ja0_61286/11_2024/9ja0_61286.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ja0_61286/11_2024/9ja0_61286.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ja0_61286/11_2024/9ja0_61286.cif" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.027 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 168 5.16 5 C 12384 2.51 5 N 3492 2.21 5 O 3672 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 19716 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1643 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 16, 'TRANS': 202} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 29 Restraints were copied for chains: C, B, E, D, G, F, I, H, K, J, L Time building chain proxies: 6.27, per 1000 atoms: 0.32 Number of scatterers: 19716 At special positions: 0 Unit cell: (106.941, 116.889, 128.495, 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 168 16.00 O 3672 8.00 N 3492 7.00 C 12384 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 198 " - pdb=" SG CYS A 218 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.16 Conformation dependent library (CDL) restraints added in 2.9 seconds 5208 Ramachandran restraints generated. 2604 Oldfield, 0 Emsley, 2604 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4944 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 12 sheets defined 67.1% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.91 Creating SS restraints... Processing helix chain 'A' and resid 16 through 30 removed outlier: 3.584A pdb=" N VAL A 27 " --> pdb=" O TRP A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 44 Processing helix chain 'A' and resid 48 through 58 Processing helix chain 'A' and resid 62 through 84 removed outlier: 3.541A pdb=" N MET A 68 " --> pdb=" O ALA A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 105 Processing helix chain 'A' and resid 110 through 120 Processing helix chain 'A' and resid 125 through 145 removed outlier: 3.701A pdb=" N LYS A 131 " --> pdb=" O GLY A 127 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS A 140 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET A 144 " --> pdb=" O LYS A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 153 removed outlier: 3.510A pdb=" N ASP A 152 " --> pdb=" O SER A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 175 Processing helix chain 'A' and resid 178 through 189 removed outlier: 3.660A pdb=" N GLU A 187 " --> pdb=" O ASN A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 204 Processing helix chain 'A' and resid 210 through 216 removed outlier: 4.165A pdb=" N THR A 216 " --> pdb=" O GLU A 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 30 removed outlier: 3.584A pdb=" N VAL B 27 " --> pdb=" O TRP B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 44 Processing helix chain 'B' and resid 48 through 58 Processing helix chain 'B' and resid 62 through 84 removed outlier: 3.541A pdb=" N MET B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 105 Processing helix chain 'B' and resid 110 through 120 Processing helix chain 'B' and resid 125 through 145 removed outlier: 3.702A pdb=" N LYS B 131 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS B 140 " --> pdb=" O LEU B 136 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET B 144 " --> pdb=" O LYS B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 153 removed outlier: 3.510A pdb=" N ASP B 152 " --> pdb=" O SER B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 175 Processing helix chain 'B' and resid 178 through 189 removed outlier: 3.660A pdb=" N GLU B 187 " --> pdb=" O ASN B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 204 Processing helix chain 'B' and resid 210 through 216 removed outlier: 4.164A pdb=" N THR B 216 " --> pdb=" O GLU B 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 30 removed outlier: 3.584A pdb=" N VAL C 27 " --> pdb=" O TRP C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 44 Processing helix chain 'C' and resid 48 through 58 Processing helix chain 'C' and resid 62 through 84 removed outlier: 3.540A pdb=" N MET C 68 " --> pdb=" O ALA C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 105 Processing helix chain 'C' and resid 110 through 120 Processing helix chain 'C' and resid 125 through 145 removed outlier: 3.701A pdb=" N LYS C 131 " --> pdb=" O GLY C 127 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS C 140 " --> pdb=" O LEU C 136 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET C 144 " --> pdb=" O LYS C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 153 removed outlier: 3.510A pdb=" N ASP C 152 " --> pdb=" O SER C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 175 Processing helix chain 'C' and resid 178 through 189 removed outlier: 3.660A pdb=" N GLU C 187 " --> pdb=" O ASN C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 204 Processing helix chain 'C' and resid 210 through 216 removed outlier: 4.165A pdb=" N THR C 216 " --> pdb=" O GLU C 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 30 removed outlier: 3.584A pdb=" N VAL D 27 " --> pdb=" O TRP D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 44 Processing helix chain 'D' and resid 48 through 58 Processing helix chain 'D' and resid 62 through 84 removed outlier: 3.540A pdb=" N MET D 68 " --> pdb=" O ALA D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 105 Processing helix chain 'D' and resid 110 through 120 Processing helix chain 'D' and resid 125 through 145 removed outlier: 3.702A pdb=" N LYS D 131 " --> pdb=" O GLY D 127 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS D 140 " --> pdb=" O LEU D 136 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET D 144 " --> pdb=" O LYS D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 153 removed outlier: 3.511A pdb=" N ASP D 152 " --> pdb=" O SER D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 175 Processing helix chain 'D' and resid 178 through 189 removed outlier: 3.659A pdb=" N GLU D 187 " --> pdb=" O ASN D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 204 Processing helix chain 'D' and resid 210 through 216 removed outlier: 4.164A pdb=" N THR D 216 " --> pdb=" O GLU D 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 30 removed outlier: 3.583A pdb=" N VAL E 27 " --> pdb=" O TRP E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 44 Processing helix chain 'E' and resid 48 through 58 Processing helix chain 'E' and resid 62 through 84 removed outlier: 3.540A pdb=" N MET E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 105 Processing helix chain 'E' and resid 110 through 120 Processing helix chain 'E' and resid 125 through 145 removed outlier: 3.702A pdb=" N LYS E 131 " --> pdb=" O GLY E 127 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS E 140 " --> pdb=" O LEU E 136 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET E 144 " --> pdb=" O LYS E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 153 removed outlier: 3.510A pdb=" N ASP E 152 " --> pdb=" O SER E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 175 Processing helix chain 'E' and resid 178 through 189 removed outlier: 3.660A pdb=" N GLU E 187 " --> pdb=" O ASN E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 204 Processing helix chain 'E' and resid 210 through 216 removed outlier: 4.165A pdb=" N THR E 216 " --> pdb=" O GLU E 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 30 removed outlier: 3.584A pdb=" N VAL F 27 " --> pdb=" O TRP F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 44 Processing helix chain 'F' and resid 48 through 58 Processing helix chain 'F' and resid 62 through 84 removed outlier: 3.541A pdb=" N MET F 68 " --> pdb=" O ALA F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 105 Processing helix chain 'F' and resid 110 through 120 Processing helix chain 'F' and resid 125 through 145 removed outlier: 3.701A pdb=" N LYS F 131 " --> pdb=" O GLY F 127 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS F 140 " --> pdb=" O LEU F 136 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET F 144 " --> pdb=" O LYS F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 149 through 153 removed outlier: 3.510A pdb=" N ASP F 152 " --> pdb=" O SER F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 175 Processing helix chain 'F' and resid 178 through 189 removed outlier: 3.659A pdb=" N GLU F 187 " --> pdb=" O ASN F 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 204 Processing helix chain 'F' and resid 210 through 216 removed outlier: 4.164A pdb=" N THR F 216 " --> pdb=" O GLU F 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 30 removed outlier: 3.583A pdb=" N VAL G 27 " --> pdb=" O TRP G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 44 Processing helix chain 'G' and resid 48 through 58 Processing helix chain 'G' and resid 62 through 84 removed outlier: 3.541A pdb=" N MET G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 105 Processing helix chain 'G' and resid 110 through 120 Processing helix chain 'G' and resid 125 through 145 removed outlier: 3.701A pdb=" N LYS G 131 " --> pdb=" O GLY G 127 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS G 140 " --> pdb=" O LEU G 136 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET G 144 " --> pdb=" O LYS G 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 153 removed outlier: 3.510A pdb=" N ASP G 152 " --> pdb=" O SER G 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 175 Processing helix chain 'G' and resid 178 through 189 removed outlier: 3.660A pdb=" N GLU G 187 " --> pdb=" O ASN G 183 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 204 Processing helix chain 'G' and resid 210 through 216 removed outlier: 4.165A pdb=" N THR G 216 " --> pdb=" O GLU G 212 " (cutoff:3.500A) Processing helix chain 'H' and resid 16 through 30 removed outlier: 3.584A pdb=" N VAL H 27 " --> pdb=" O TRP H 23 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 44 Processing helix chain 'H' and resid 48 through 58 Processing helix chain 'H' and resid 62 through 84 removed outlier: 3.541A pdb=" N MET H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 105 Processing helix chain 'H' and resid 110 through 120 Processing helix chain 'H' and resid 125 through 145 removed outlier: 3.702A pdb=" N LYS H 131 " --> pdb=" O GLY H 127 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS H 140 " --> pdb=" O LEU H 136 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET H 144 " --> pdb=" O LYS H 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 149 through 153 removed outlier: 3.510A pdb=" N ASP H 152 " --> pdb=" O SER H 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 175 Processing helix chain 'H' and resid 178 through 189 removed outlier: 3.659A pdb=" N GLU H 187 " --> pdb=" O ASN H 183 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 204 Processing helix chain 'H' and resid 210 through 216 removed outlier: 4.164A pdb=" N THR H 216 " --> pdb=" O GLU H 212 " (cutoff:3.500A) Processing helix chain 'I' and resid 16 through 30 removed outlier: 3.583A pdb=" N VAL I 27 " --> pdb=" O TRP I 23 " (cutoff:3.500A) Processing helix chain 'I' and resid 35 through 44 Processing helix chain 'I' and resid 48 through 58 Processing helix chain 'I' and resid 62 through 84 removed outlier: 3.541A pdb=" N MET I 68 " --> pdb=" O ALA I 64 " (cutoff:3.500A) Processing helix chain 'I' and resid 100 through 105 Processing helix chain 'I' and resid 110 through 120 Processing helix chain 'I' and resid 125 through 145 removed outlier: 3.701A pdb=" N LYS I 131 " --> pdb=" O GLY I 127 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS I 140 " --> pdb=" O LEU I 136 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET I 144 " --> pdb=" O LYS I 140 " (cutoff:3.500A) Processing helix chain 'I' and resid 149 through 153 removed outlier: 3.511A pdb=" N ASP I 152 " --> pdb=" O SER I 149 " (cutoff:3.500A) Processing helix chain 'I' and resid 160 through 175 Processing helix chain 'I' and resid 178 through 189 removed outlier: 3.660A pdb=" N GLU I 187 " --> pdb=" O ASN I 183 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 204 Processing helix chain 'I' and resid 210 through 216 removed outlier: 4.164A pdb=" N THR I 216 " --> pdb=" O GLU I 212 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 30 removed outlier: 3.583A pdb=" N VAL J 27 " --> pdb=" O TRP J 23 " (cutoff:3.500A) Processing helix chain 'J' and resid 35 through 44 Processing helix chain 'J' and resid 48 through 58 Processing helix chain 'J' and resid 62 through 84 removed outlier: 3.542A pdb=" N MET J 68 " --> pdb=" O ALA J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 100 through 105 Processing helix chain 'J' and resid 110 through 120 Processing helix chain 'J' and resid 125 through 145 removed outlier: 3.701A pdb=" N LYS J 131 " --> pdb=" O GLY J 127 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS J 140 " --> pdb=" O LEU J 136 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET J 144 " --> pdb=" O LYS J 140 " (cutoff:3.500A) Processing helix chain 'J' and resid 149 through 153 removed outlier: 3.510A pdb=" N ASP J 152 " --> pdb=" O SER J 149 " (cutoff:3.500A) Processing helix chain 'J' and resid 160 through 175 Processing helix chain 'J' and resid 178 through 189 removed outlier: 3.660A pdb=" N GLU J 187 " --> pdb=" O ASN J 183 " (cutoff:3.500A) Processing helix chain 'J' and resid 195 through 204 Processing helix chain 'J' and resid 210 through 216 removed outlier: 4.164A pdb=" N THR J 216 " --> pdb=" O GLU J 212 " (cutoff:3.500A) Processing helix chain 'K' and resid 16 through 30 removed outlier: 3.584A pdb=" N VAL K 27 " --> pdb=" O TRP K 23 " (cutoff:3.500A) Processing helix chain 'K' and resid 35 through 44 Processing helix chain 'K' and resid 48 through 58 Processing helix chain 'K' and resid 62 through 84 removed outlier: 3.541A pdb=" N MET K 68 " --> pdb=" O ALA K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 100 through 105 Processing helix chain 'K' and resid 110 through 120 Processing helix chain 'K' and resid 125 through 145 removed outlier: 3.702A pdb=" N LYS K 131 " --> pdb=" O GLY K 127 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS K 140 " --> pdb=" O LEU K 136 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET K 144 " --> pdb=" O LYS K 140 " (cutoff:3.500A) Processing helix chain 'K' and resid 149 through 153 removed outlier: 3.511A pdb=" N ASP K 152 " --> pdb=" O SER K 149 " (cutoff:3.500A) Processing helix chain 'K' and resid 160 through 175 Processing helix chain 'K' and resid 178 through 189 removed outlier: 3.660A pdb=" N GLU K 187 " --> pdb=" O ASN K 183 " (cutoff:3.500A) Processing helix chain 'K' and resid 195 through 204 Processing helix chain 'K' and resid 210 through 216 removed outlier: 4.164A pdb=" N THR K 216 " --> pdb=" O GLU K 212 " (cutoff:3.500A) Processing helix chain 'L' and resid 16 through 30 removed outlier: 3.583A pdb=" N VAL L 27 " --> pdb=" O TRP L 23 " (cutoff:3.500A) Processing helix chain 'L' and resid 35 through 44 Processing helix chain 'L' and resid 48 through 58 Processing helix chain 'L' and resid 62 through 84 removed outlier: 3.540A pdb=" N MET L 68 " --> pdb=" O ALA L 64 " (cutoff:3.500A) Processing helix chain 'L' and resid 100 through 105 Processing helix chain 'L' and resid 110 through 120 Processing helix chain 'L' and resid 125 through 145 removed outlier: 3.701A pdb=" N LYS L 131 " --> pdb=" O GLY L 127 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS L 140 " --> pdb=" O LEU L 136 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET L 144 " --> pdb=" O LYS L 140 " (cutoff:3.500A) Processing helix chain 'L' and resid 149 through 153 removed outlier: 3.510A pdb=" N ASP L 152 " --> pdb=" O SER L 149 " (cutoff:3.500A) Processing helix chain 'L' and resid 160 through 175 Processing helix chain 'L' and resid 178 through 189 removed outlier: 3.660A pdb=" N GLU L 187 " --> pdb=" O ASN L 183 " (cutoff:3.500A) Processing helix chain 'L' and resid 195 through 204 Processing helix chain 'L' and resid 210 through 216 removed outlier: 4.165A pdb=" N THR L 216 " --> pdb=" O GLU L 212 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 4 Processing sheet with id=AA2, first strand: chain 'B' and resid 2 through 4 Processing sheet with id=AA3, first strand: chain 'C' and resid 2 through 4 Processing sheet with id=AA4, first strand: chain 'D' and resid 2 through 4 Processing sheet with id=AA5, first strand: chain 'E' and resid 2 through 4 Processing sheet with id=AA6, first strand: chain 'F' and resid 2 through 4 Processing sheet with id=AA7, first strand: chain 'G' and resid 2 through 4 Processing sheet with id=AA8, first strand: chain 'H' and resid 2 through 4 Processing sheet with id=AA9, first strand: chain 'I' and resid 2 through 4 Processing sheet with id=AB1, first strand: chain 'J' and resid 2 through 4 Processing sheet with id=AB2, first strand: chain 'K' and resid 2 through 4 Processing sheet with id=AB3, first strand: chain 'L' and resid 2 through 4 1128 hydrogen bonds defined for protein. 3348 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: 5.64 Time building geometry restraints manager: 5.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6673 1.34 - 1.46: 3267 1.46 - 1.58: 9860 1.58 - 1.69: 0 1.69 - 1.81: 288 Bond restraints: 20088 Sorted by residual: bond pdb=" C ILE G 37 " pdb=" O ILE G 37 " ideal model delta sigma weight residual 1.242 1.227 0.015 8.60e-03 1.35e+04 2.92e+00 bond pdb=" C ILE E 37 " pdb=" O ILE E 37 " ideal model delta sigma weight residual 1.242 1.227 0.015 8.60e-03 1.35e+04 2.87e+00 bond pdb=" C ILE L 37 " pdb=" O ILE L 37 " ideal model delta sigma weight residual 1.242 1.227 0.015 8.60e-03 1.35e+04 2.87e+00 bond pdb=" C ILE C 37 " pdb=" O ILE C 37 " ideal model delta sigma weight residual 1.242 1.227 0.015 8.60e-03 1.35e+04 2.87e+00 bond pdb=" C ILE D 37 " pdb=" O ILE D 37 " ideal model delta sigma weight residual 1.242 1.228 0.014 8.60e-03 1.35e+04 2.74e+00 ... (remaining 20083 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 26098 1.40 - 2.80: 972 2.80 - 4.20: 194 4.20 - 5.60: 36 5.60 - 7.01: 24 Bond angle restraints: 27324 Sorted by residual: angle pdb=" N PRO I 122 " pdb=" CA PRO I 122 " pdb=" C PRO I 122 " ideal model delta sigma weight residual 110.70 103.69 7.01 1.22e+00 6.72e-01 3.30e+01 angle pdb=" N PRO G 122 " pdb=" CA PRO G 122 " pdb=" C PRO G 122 " ideal model delta sigma weight residual 110.70 103.70 7.00 1.22e+00 6.72e-01 3.29e+01 angle pdb=" N PRO L 122 " pdb=" CA PRO L 122 " pdb=" C PRO L 122 " ideal model delta sigma weight residual 110.70 103.71 6.99 1.22e+00 6.72e-01 3.29e+01 angle pdb=" N PRO C 122 " pdb=" CA PRO C 122 " pdb=" C PRO C 122 " ideal model delta sigma weight residual 110.70 103.71 6.99 1.22e+00 6.72e-01 3.29e+01 angle pdb=" N PRO D 122 " pdb=" CA PRO D 122 " pdb=" C PRO D 122 " ideal model delta sigma weight residual 110.70 103.73 6.97 1.22e+00 6.72e-01 3.27e+01 ... (remaining 27319 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.78: 10995 13.78 - 27.56: 971 27.56 - 41.34: 205 41.34 - 55.12: 72 55.12 - 68.90: 24 Dihedral angle restraints: 12267 sinusoidal: 4659 harmonic: 7608 Sorted by residual: dihedral pdb=" CG ARG F 143 " pdb=" CD ARG F 143 " pdb=" NE ARG F 143 " pdb=" CZ ARG F 143 " ideal model delta sinusoidal sigma weight residual 180.00 138.07 41.93 2 1.50e+01 4.44e-03 9.53e+00 dihedral pdb=" CG ARG C 143 " pdb=" CD ARG C 143 " pdb=" NE ARG C 143 " pdb=" CZ ARG C 143 " ideal model delta sinusoidal sigma weight residual 180.00 138.09 41.91 2 1.50e+01 4.44e-03 9.52e+00 dihedral pdb=" CG ARG E 143 " pdb=" CD ARG E 143 " pdb=" NE ARG E 143 " pdb=" CZ ARG E 143 " ideal model delta sinusoidal sigma weight residual 180.00 138.11 41.89 2 1.50e+01 4.44e-03 9.51e+00 ... (remaining 12264 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2057 0.035 - 0.070: 805 0.070 - 0.105: 209 0.105 - 0.140: 61 0.140 - 0.174: 36 Chirality restraints: 3168 Sorted by residual: chirality pdb=" CA ILE C 124 " pdb=" N ILE C 124 " pdb=" C ILE C 124 " pdb=" CB ILE C 124 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.61e-01 chirality pdb=" CA ILE F 124 " pdb=" N ILE F 124 " pdb=" C ILE F 124 " pdb=" CB ILE F 124 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.53e-01 chirality pdb=" CA ILE A 124 " pdb=" N ILE A 124 " pdb=" C ILE A 124 " pdb=" CB ILE A 124 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.41e-01 ... (remaining 3165 not shown) Planarity restraints: 3552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR G 48 " 0.032 5.00e-02 4.00e+02 4.86e-02 3.77e+00 pdb=" N PRO G 49 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 48 " -0.032 5.00e-02 4.00e+02 4.85e-02 3.77e+00 pdb=" N PRO C 49 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO C 49 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 49 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR J 48 " -0.032 5.00e-02 4.00e+02 4.85e-02 3.77e+00 pdb=" N PRO J 49 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO J 49 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO J 49 " -0.027 5.00e-02 4.00e+02 ... (remaining 3549 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 130 2.55 - 3.14: 14979 3.14 - 3.72: 30098 3.72 - 4.31: 42841 4.31 - 4.90: 68325 Nonbonded interactions: 156373 Sorted by model distance: nonbonded pdb=" SG CYS A 14 " pdb=" SG CYS B 45 " model vdw 1.961 3.760 nonbonded pdb=" SG CYS E 14 " pdb=" SG CYS F 45 " model vdw 1.997 3.760 nonbonded pdb=" SG CYS H 45 " pdb=" SG CYS I 14 " model vdw 2.000 3.760 nonbonded pdb=" SG CYS D 45 " pdb=" SG CYS F 14 " model vdw 2.000 3.760 nonbonded pdb=" SG CYS C 45 " pdb=" SG CYS D 14 " model vdw 2.006 3.760 ... (remaining 156368 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.750 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 38.500 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 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 0.035 20088 Z= 0.223 Angle : 0.668 7.005 27324 Z= 0.438 Chirality : 0.044 0.174 3168 Planarity : 0.006 0.049 3552 Dihedral : 11.921 68.899 7320 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.28 (0.12), residues: 2604 helix: -3.25 (0.08), residues: 1620 sheet: None (None), residues: 0 loop : -1.74 (0.17), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 117 HIS 0.002 0.001 HIS F 12 PHE 0.015 0.002 PHE B 32 TYR 0.006 0.001 TYR C 130 ARG 0.003 0.001 ARG F 154 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5208 Ramachandran restraints generated. 2604 Oldfield, 0 Emsley, 2604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5208 Ramachandran restraints generated. 2604 Oldfield, 0 Emsley, 2604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 363 time to evaluate : 2.205 Fit side-chains REVERT: A 112 GLN cc_start: 0.7809 (mp-120) cc_final: 0.7564 (mp10) REVERT: C 4 GLN cc_start: 0.7971 (tt0) cc_final: 0.7351 (tm-30) REVERT: D 112 GLN cc_start: 0.7773 (mp-120) cc_final: 0.7489 (mp-120) REVERT: E 4 GLN cc_start: 0.7976 (tt0) cc_final: 0.7334 (tm-30) REVERT: F 112 GLN cc_start: 0.7727 (mp-120) cc_final: 0.7444 (mp10) REVERT: H 112 GLN cc_start: 0.7712 (mp-120) cc_final: 0.7432 (mp10) REVERT: J 39 MET cc_start: 0.8717 (tpt) cc_final: 0.8516 (tpp) REVERT: J 112 GLN cc_start: 0.7777 (mp-120) cc_final: 0.7490 (mp-120) REVERT: K 112 GLN cc_start: 0.7742 (mp-120) cc_final: 0.7469 (mp10) REVERT: L 4 GLN cc_start: 0.7971 (tt0) cc_final: 0.7339 (tm-30) outliers start: 0 outliers final: 0 residues processed: 363 average time/residue: 0.2777 time to fit residues: 155.2223 Evaluate side-chains 280 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 280 time to evaluate : 1.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 102 optimal weight: 9.9990 chunk 197 optimal weight: 5.9990 chunk 76 optimal weight: 0.7980 chunk 120 optimal weight: 5.9990 chunk 147 optimal weight: 0.0570 chunk 228 optimal weight: 8.9990 overall best weight: 1.5704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN A 193 ASN B 4 GLN B 193 ASN C 112 GLN C 193 ASN D 4 GLN D 193 ASN E 193 ASN F 4 GLN F 193 ASN G 4 GLN G 193 ASN H 4 GLN H 193 ASN I 4 GLN I 193 ASN J 4 GLN J 193 ASN K 4 GLN K 193 ASN L 193 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 20088 Z= 0.294 Angle : 0.563 5.795 27324 Z= 0.295 Chirality : 0.045 0.129 3168 Planarity : 0.005 0.039 3552 Dihedral : 4.207 19.207 2784 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.75 % Allowed : 7.34 % Favored : 91.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.15), residues: 2604 helix: -0.87 (0.11), residues: 1644 sheet: None (None), residues: 0 loop : -1.52 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP F 117 HIS 0.003 0.001 HIS G 84 PHE 0.014 0.002 PHE A 32 TYR 0.014 0.002 TYR B 130 ARG 0.002 0.001 ARG D 167 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5208 Ramachandran restraints generated. 2604 Oldfield, 0 Emsley, 2604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5208 Ramachandran restraints generated. 2604 Oldfield, 0 Emsley, 2604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 303 time to evaluate : 2.469 Fit side-chains REVERT: B 82 ARG cc_start: 0.7629 (ttp80) cc_final: 0.7380 (ttp80) REVERT: D 82 ARG cc_start: 0.7634 (ttp80) cc_final: 0.7386 (ttp80) REVERT: G 82 ARG cc_start: 0.7633 (ttp80) cc_final: 0.7384 (ttp80) REVERT: J 82 ARG cc_start: 0.7628 (ttp80) cc_final: 0.7379 (ttp80) outliers start: 15 outliers final: 12 residues processed: 309 average time/residue: 0.3140 time to fit residues: 147.0166 Evaluate side-chains 311 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 299 time to evaluate : 1.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 136 LEU Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain L residue 11 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 127 optimal weight: 0.9990 chunk 71 optimal weight: 7.9990 chunk 190 optimal weight: 0.9990 chunk 155 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 229 optimal weight: 10.0000 chunk 247 optimal weight: 0.6980 chunk 204 optimal weight: 9.9990 chunk 227 optimal weight: 7.9990 chunk 78 optimal weight: 8.9990 chunk 183 optimal weight: 8.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN C 4 GLN E 4 GLN F 4 GLN H 4 GLN I 4 GLN K 4 GLN L 4 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 20088 Z= 0.317 Angle : 0.537 5.868 27324 Z= 0.273 Chirality : 0.045 0.143 3168 Planarity : 0.005 0.038 3552 Dihedral : 4.267 20.993 2784 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.75 % Allowed : 10.73 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.15), residues: 2604 helix: 0.10 (0.12), residues: 1644 sheet: None (None), residues: 0 loop : -1.48 (0.18), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 80 HIS 0.003 0.001 HIS I 84 PHE 0.012 0.002 PHE A 32 TYR 0.011 0.002 TYR D 130 ARG 0.006 0.001 ARG A 154 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5208 Ramachandran restraints generated. 2604 Oldfield, 0 Emsley, 2604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5208 Ramachandran restraints generated. 2604 Oldfield, 0 Emsley, 2604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 269 time to evaluate : 2.472 Fit side-chains REVERT: C 118 MET cc_start: 0.8859 (mtt) cc_final: 0.8659 (mtt) REVERT: E 118 MET cc_start: 0.8862 (mtt) cc_final: 0.8656 (mtt) REVERT: I 118 MET cc_start: 0.8846 (mtt) cc_final: 0.8641 (mtt) REVERT: L 118 MET cc_start: 0.8858 (mtt) cc_final: 0.8654 (mtt) outliers start: 35 outliers final: 35 residues processed: 289 average time/residue: 0.3496 time to fit residues: 153.0548 Evaluate side-chains 306 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 271 time to evaluate : 2.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain G residue 218 CYS Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 136 LEU Chi-restraints excluded: chain H residue 144 MET Chi-restraints excluded: chain I residue 102 SER Chi-restraints excluded: chain I residue 144 MET Chi-restraints excluded: chain I residue 218 CYS Chi-restraints excluded: chain J residue 144 MET Chi-restraints excluded: chain J residue 218 CYS Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 102 SER Chi-restraints excluded: chain K residue 136 LEU Chi-restraints excluded: chain K residue 144 MET Chi-restraints excluded: chain K residue 218 CYS Chi-restraints excluded: chain L residue 102 SER Chi-restraints excluded: chain L residue 144 MET Chi-restraints excluded: chain L residue 218 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 226 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 109 optimal weight: 0.8980 chunk 153 optimal weight: 2.9990 chunk 230 optimal weight: 3.9990 chunk 243 optimal weight: 1.9990 chunk 120 optimal weight: 0.0370 chunk 218 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 overall best weight: 0.9460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN B 112 GLN H 4 GLN K 4 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 20088 Z= 0.192 Angle : 0.455 5.031 27324 Z= 0.230 Chirality : 0.042 0.132 3168 Planarity : 0.004 0.038 3552 Dihedral : 4.049 19.496 2784 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.15 % Allowed : 11.53 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.16), residues: 2604 helix: 0.76 (0.13), residues: 1644 sheet: None (None), residues: 0 loop : -1.43 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 23 HIS 0.001 0.001 HIS H 12 PHE 0.011 0.001 PHE H 32 TYR 0.009 0.001 TYR A 169 ARG 0.006 0.000 ARG A 154 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5208 Ramachandran restraints generated. 2604 Oldfield, 0 Emsley, 2604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5208 Ramachandran restraints generated. 2604 Oldfield, 0 Emsley, 2604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 285 time to evaluate : 3.373 Fit side-chains REVERT: C 103 ASP cc_start: 0.8309 (m-30) cc_final: 0.8052 (m-30) REVERT: E 82 ARG cc_start: 0.7613 (ttp80) cc_final: 0.7399 (ttp80) REVERT: I 82 ARG cc_start: 0.7612 (ttp80) cc_final: 0.7395 (ttp80) REVERT: L 103 ASP cc_start: 0.8306 (m-30) cc_final: 0.8050 (m-30) outliers start: 23 outliers final: 18 residues processed: 300 average time/residue: 0.3359 time to fit residues: 156.6084 Evaluate side-chains 291 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 273 time to evaluate : 2.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain G residue 102 SER Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain I residue 102 SER Chi-restraints excluded: chain I residue 144 MET Chi-restraints excluded: chain J residue 102 SER Chi-restraints excluded: chain L residue 102 SER Chi-restraints excluded: chain L residue 144 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 202 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 181 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 207 optimal weight: 6.9990 chunk 168 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 124 optimal weight: 9.9990 chunk 218 optimal weight: 6.9990 chunk 61 optimal weight: 7.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN C 4 GLN E 4 GLN F 4 GLN H 4 GLN K 4 GLN L 4 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 20088 Z= 0.290 Angle : 0.491 4.567 27324 Z= 0.247 Chirality : 0.045 0.136 3168 Planarity : 0.004 0.038 3552 Dihedral : 4.168 20.161 2784 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.60 % Allowed : 11.68 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.16), residues: 2604 helix: 0.92 (0.13), residues: 1644 sheet: None (None), residues: 0 loop : -1.39 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 80 HIS 0.002 0.001 HIS J 84 PHE 0.012 0.002 PHE A 32 TYR 0.008 0.002 TYR D 169 ARG 0.007 0.001 ARG A 154 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5208 Ramachandran restraints generated. 2604 Oldfield, 0 Emsley, 2604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5208 Ramachandran restraints generated. 2604 Oldfield, 0 Emsley, 2604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 262 time to evaluate : 2.333 Fit side-chains outliers start: 32 outliers final: 25 residues processed: 274 average time/residue: 0.3713 time to fit residues: 148.5798 Evaluate side-chains 283 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 258 time to evaluate : 2.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 144 MET Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 102 SER Chi-restraints excluded: chain I residue 144 MET Chi-restraints excluded: chain J residue 144 MET Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 136 LEU Chi-restraints excluded: chain K residue 144 MET Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 102 SER Chi-restraints excluded: chain L residue 144 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 81 optimal weight: 2.9990 chunk 219 optimal weight: 9.9990 chunk 48 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 243 optimal weight: 2.9990 chunk 202 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 80 optimal weight: 0.9980 chunk 128 optimal weight: 3.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN A 176 GLN D 176 GLN H 4 GLN H 176 GLN J 176 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 20088 Z= 0.349 Angle : 0.521 4.657 27324 Z= 0.264 Chirality : 0.046 0.138 3168 Planarity : 0.005 0.037 3552 Dihedral : 4.281 21.433 2784 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.55 % Allowed : 12.52 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.16), residues: 2604 helix: 0.90 (0.13), residues: 1644 sheet: None (None), residues: 0 loop : -1.30 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 80 HIS 0.003 0.001 HIS D 84 PHE 0.010 0.002 PHE H 32 TYR 0.008 0.002 TYR J 169 ARG 0.007 0.001 ARG A 154 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5208 Ramachandran restraints generated. 2604 Oldfield, 0 Emsley, 2604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5208 Ramachandran restraints generated. 2604 Oldfield, 0 Emsley, 2604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 271 time to evaluate : 2.328 Fit side-chains REVERT: C 10 MET cc_start: 0.8042 (mmm) cc_final: 0.7809 (mmm) REVERT: L 10 MET cc_start: 0.8045 (mmm) cc_final: 0.7811 (mmm) outliers start: 31 outliers final: 30 residues processed: 285 average time/residue: 0.3758 time to fit residues: 156.3435 Evaluate side-chains 295 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 265 time to evaluate : 2.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain G residue 102 SER Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 136 LEU Chi-restraints excluded: chain H residue 144 MET Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 102 SER Chi-restraints excluded: chain I residue 144 MET Chi-restraints excluded: chain J residue 144 MET Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 136 LEU Chi-restraints excluded: chain K residue 144 MET Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 102 SER Chi-restraints excluded: chain L residue 144 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 235 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 138 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 chunk 137 optimal weight: 0.7980 chunk 205 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 chunk 242 optimal weight: 1.9990 chunk 152 optimal weight: 0.0570 chunk 148 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 overall best weight: 0.9700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 20088 Z= 0.197 Angle : 0.449 4.473 27324 Z= 0.228 Chirality : 0.043 0.135 3168 Planarity : 0.004 0.036 3552 Dihedral : 4.098 19.855 2784 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.45 % Allowed : 11.88 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.16), residues: 2604 helix: 1.16 (0.13), residues: 1644 sheet: None (None), residues: 0 loop : -1.24 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 23 HIS 0.002 0.001 HIS D 84 PHE 0.010 0.002 PHE H 32 TYR 0.009 0.001 TYR D 169 ARG 0.007 0.000 ARG C 154 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5208 Ramachandran restraints generated. 2604 Oldfield, 0 Emsley, 2604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5208 Ramachandran restraints generated. 2604 Oldfield, 0 Emsley, 2604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 272 time to evaluate : 2.134 Fit side-chains REVERT: B 154 ARG cc_start: 0.7671 (mtt-85) cc_final: 0.7330 (mtt-85) REVERT: C 154 ARG cc_start: 0.7606 (mtt-85) cc_final: 0.7352 (mtt-85) REVERT: D 154 ARG cc_start: 0.7675 (mtt-85) cc_final: 0.7332 (mtt-85) REVERT: E 154 ARG cc_start: 0.7589 (mtt-85) cc_final: 0.7316 (mtt-85) REVERT: G 154 ARG cc_start: 0.7688 (mtt-85) cc_final: 0.7365 (mtt-85) REVERT: I 154 ARG cc_start: 0.7595 (mtt-85) cc_final: 0.7318 (mtt-85) REVERT: L 154 ARG cc_start: 0.7607 (mtt-85) cc_final: 0.7353 (mtt-85) outliers start: 29 outliers final: 28 residues processed: 284 average time/residue: 0.3817 time to fit residues: 157.6770 Evaluate side-chains 291 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 263 time to evaluate : 2.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain G residue 102 SER Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain H residue 136 LEU Chi-restraints excluded: chain H residue 144 MET Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 102 SER Chi-restraints excluded: chain I residue 144 MET Chi-restraints excluded: chain J residue 144 MET Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 136 LEU Chi-restraints excluded: chain K residue 144 MET Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 102 SER Chi-restraints excluded: chain L residue 144 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 150 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 145 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 165 optimal weight: 8.9990 chunk 120 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 190 optimal weight: 2.9990 chunk 220 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 176 GLN ** D 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 176 GLN F 4 GLN F 176 GLN I 176 GLN ** J 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 4 GLN L 176 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 20088 Z= 0.379 Angle : 0.530 4.692 27324 Z= 0.268 Chirality : 0.047 0.140 3168 Planarity : 0.005 0.036 3552 Dihedral : 4.294 21.644 2784 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.45 % Allowed : 13.42 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.16), residues: 2604 helix: 1.00 (0.13), residues: 1644 sheet: None (None), residues: 0 loop : -1.12 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 80 HIS 0.003 0.001 HIS G 84 PHE 0.011 0.002 PHE H 32 TYR 0.008 0.002 TYR G 169 ARG 0.007 0.001 ARG F 154 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5208 Ramachandran restraints generated. 2604 Oldfield, 0 Emsley, 2604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5208 Ramachandran restraints generated. 2604 Oldfield, 0 Emsley, 2604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 273 time to evaluate : 2.209 Fit side-chains REVERT: B 154 ARG cc_start: 0.7706 (mtt-85) cc_final: 0.7406 (mtt-85) REVERT: C 10 MET cc_start: 0.8039 (mmm) cc_final: 0.7808 (mmm) REVERT: D 154 ARG cc_start: 0.7695 (mtt-85) cc_final: 0.7378 (mtt-85) REVERT: G 154 ARG cc_start: 0.7711 (mtt-85) cc_final: 0.7412 (mtt-85) REVERT: J 154 ARG cc_start: 0.7708 (mtt-85) cc_final: 0.7427 (mtt-85) REVERT: L 10 MET cc_start: 0.8038 (mmm) cc_final: 0.7811 (mmm) outliers start: 29 outliers final: 28 residues processed: 286 average time/residue: 0.3760 time to fit residues: 156.7021 Evaluate side-chains 294 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 266 time to evaluate : 2.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain G residue 102 SER Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 136 LEU Chi-restraints excluded: chain H residue 144 MET Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 102 SER Chi-restraints excluded: chain I residue 144 MET Chi-restraints excluded: chain J residue 102 SER Chi-restraints excluded: chain K residue 136 LEU Chi-restraints excluded: chain K residue 144 MET Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 102 SER Chi-restraints excluded: chain L residue 144 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 232 optimal weight: 1.9990 chunk 212 optimal weight: 0.9980 chunk 226 optimal weight: 0.7980 chunk 136 optimal weight: 4.9990 chunk 98 optimal weight: 0.4980 chunk 177 optimal weight: 8.9990 chunk 69 optimal weight: 0.7980 chunk 204 optimal weight: 0.0170 chunk 214 optimal weight: 0.8980 chunk 225 optimal weight: 10.0000 chunk 148 optimal weight: 4.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 20088 Z= 0.150 Angle : 0.431 4.739 27324 Z= 0.219 Chirality : 0.042 0.133 3168 Planarity : 0.004 0.037 3552 Dihedral : 3.992 20.144 2784 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.45 % Allowed : 12.48 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.17), residues: 2604 helix: 1.39 (0.13), residues: 1644 sheet: None (None), residues: 0 loop : -1.16 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 23 HIS 0.001 0.000 HIS E 84 PHE 0.007 0.001 PHE H 32 TYR 0.010 0.001 TYR D 169 ARG 0.007 0.000 ARG K 154 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5208 Ramachandran restraints generated. 2604 Oldfield, 0 Emsley, 2604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5208 Ramachandran restraints generated. 2604 Oldfield, 0 Emsley, 2604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 284 time to evaluate : 2.242 Fit side-chains REVERT: B 82 ARG cc_start: 0.7837 (ttp80) cc_final: 0.7452 (ttp80) REVERT: B 154 ARG cc_start: 0.7695 (mtt-85) cc_final: 0.7443 (mtt-85) REVERT: C 103 ASP cc_start: 0.8327 (m-30) cc_final: 0.8066 (m-30) REVERT: D 82 ARG cc_start: 0.7839 (ttp80) cc_final: 0.7458 (ttp80) REVERT: D 154 ARG cc_start: 0.7697 (mtt-85) cc_final: 0.7450 (mtt-85) REVERT: E 103 ASP cc_start: 0.8323 (m-30) cc_final: 0.8025 (m-30) REVERT: G 82 ARG cc_start: 0.7835 (ttp80) cc_final: 0.7449 (ttp80) REVERT: G 154 ARG cc_start: 0.7702 (mtt-85) cc_final: 0.7457 (mtt-85) REVERT: I 103 ASP cc_start: 0.8324 (m-30) cc_final: 0.8018 (m-30) REVERT: J 82 ARG cc_start: 0.7848 (ttp80) cc_final: 0.7464 (ttp80) REVERT: J 154 ARG cc_start: 0.7702 (mtt-85) cc_final: 0.7428 (mtt-85) REVERT: L 103 ASP cc_start: 0.8330 (m-30) cc_final: 0.8070 (m-30) outliers start: 29 outliers final: 24 residues processed: 296 average time/residue: 0.3750 time to fit residues: 160.1867 Evaluate side-chains 287 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 263 time to evaluate : 2.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain G residue 102 SER Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain H residue 144 MET Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 102 SER Chi-restraints excluded: chain I residue 144 MET Chi-restraints excluded: chain J residue 102 SER Chi-restraints excluded: chain J residue 144 MET Chi-restraints excluded: chain K residue 144 MET Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 102 SER Chi-restraints excluded: chain L residue 144 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 239 optimal weight: 1.9990 chunk 146 optimal weight: 0.0770 chunk 113 optimal weight: 4.9990 chunk 166 optimal weight: 7.9990 chunk 251 optimal weight: 0.3980 chunk 231 optimal weight: 4.9990 chunk 199 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 154 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 158 optimal weight: 0.6980 overall best weight: 1.0342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 176 GLN F 4 GLN ** I 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 4 GLN L 176 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20088 Z= 0.208 Angle : 0.451 4.620 27324 Z= 0.227 Chirality : 0.043 0.132 3168 Planarity : 0.004 0.037 3552 Dihedral : 4.011 20.334 2784 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.10 % Allowed : 13.87 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.17), residues: 2604 helix: 1.42 (0.13), residues: 1644 sheet: None (None), residues: 0 loop : -1.10 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 80 HIS 0.002 0.001 HIS E 84 PHE 0.011 0.002 PHE H 32 TYR 0.008 0.001 TYR D 169 ARG 0.008 0.000 ARG H 154 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5208 Ramachandran restraints generated. 2604 Oldfield, 0 Emsley, 2604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5208 Ramachandran restraints generated. 2604 Oldfield, 0 Emsley, 2604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 268 time to evaluate : 2.292 Fit side-chains REVERT: B 154 ARG cc_start: 0.7702 (mtt-85) cc_final: 0.7423 (mtt-85) REVERT: D 154 ARG cc_start: 0.7706 (mtt-85) cc_final: 0.7442 (mtt-85) REVERT: G 154 ARG cc_start: 0.7711 (mtt-85) cc_final: 0.7451 (mtt-85) REVERT: J 154 ARG cc_start: 0.7710 (mtt-85) cc_final: 0.7437 (mtt-85) REVERT: L 189 LEU cc_start: 0.8082 (tp) cc_final: 0.7850 (tp) outliers start: 22 outliers final: 22 residues processed: 275 average time/residue: 0.3862 time to fit residues: 153.0299 Evaluate side-chains 287 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 265 time to evaluate : 2.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain G residue 102 SER Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain H residue 144 MET Chi-restraints excluded: chain I residue 144 MET Chi-restraints excluded: chain J residue 102 SER Chi-restraints excluded: chain J residue 144 MET Chi-restraints excluded: chain K residue 144 MET Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 102 SER Chi-restraints excluded: chain L residue 144 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 184 optimal weight: 0.5980 chunk 29 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 chunk 200 optimal weight: 0.7980 chunk 83 optimal weight: 0.0970 chunk 205 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 175 optimal weight: 2.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.185403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.132245 restraints weight = 20397.412| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.58 r_work: 0.3337 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 20088 Z= 0.154 Angle : 0.429 4.646 27324 Z= 0.217 Chirality : 0.042 0.130 3168 Planarity : 0.004 0.037 3552 Dihedral : 3.908 19.754 2784 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.05 % Allowed : 13.77 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.17), residues: 2604 helix: 1.57 (0.13), residues: 1644 sheet: None (None), residues: 0 loop : -1.11 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 23 HIS 0.001 0.000 HIS C 84 PHE 0.009 0.001 PHE H 32 TYR 0.009 0.001 TYR D 169 ARG 0.008 0.000 ARG F 154 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4044.25 seconds wall clock time: 188 minutes 40.29 seconds (11320.29 seconds total)