Starting phenix.real_space_refine on Sat May 11 16:44:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qyj_18755/05_2024/8qyj_18755_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qyj_18755/05_2024/8qyj_18755.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qyj_18755/05_2024/8qyj_18755.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qyj_18755/05_2024/8qyj_18755.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qyj_18755/05_2024/8qyj_18755_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qyj_18755/05_2024/8qyj_18755_updated.pdb" } resolution = 2.73 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= 0.008 sd= 0.129 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 114 5.16 5 C 12336 2.51 5 N 3306 2.21 5 O 3646 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 120": "OE1" <-> "OE2" Residue "A PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 130": "OE1" <-> "OE2" Residue "G GLU 174": "OE1" <-> "OE2" Residue "G GLU 180": "OE1" <-> "OE2" Residue "H GLU 82": "OE1" <-> "OE2" Residue "J GLU 65": "OE1" <-> "OE2" Residue "J GLU 76": "OE1" <-> "OE2" Residue "L GLU 107": "OE1" <-> "OE2" Residue "M GLU 114": "OE1" <-> "OE2" Residue "M GLU 121": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 19402 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1766 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 217} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 1841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1841 Classifications: {'peptide': 236} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 230} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 1847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1847 Classifications: {'peptide': 236} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 229} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1848 Unusual residues: {'ACE': 1} Classifications: {'peptide': 241, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 8, 'TRANS': 232} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 1886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1886 Unusual residues: {'ACE': 1} Classifications: {'peptide': 239, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 9, 'TRANS': 229} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 1872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1872 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 234} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1787 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 8, 'TRANS': 226} Chain breaks: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 6, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "H" Number of atoms: 408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 408 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 49} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 1933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1933 Classifications: {'peptide': 243} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 231} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "J" Number of atoms: 1909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1909 Unusual residues: {'ACE': 1} Classifications: {'peptide': 247, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'ACE_C-N': 1, 'PTRANS': 15, 'TRANS': 231} Chain breaks: 2 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "K" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 512 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain breaks: 3 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "L" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "M" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 908 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 109} Time building chain proxies: 11.07, per 1000 atoms: 0.57 Number of scatterers: 19402 At special positions: 0 Unit cell: (123.424, 141.299, 133.638, 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 114 16.00 O 3646 8.00 N 3306 7.00 C 12336 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 7.07 Conformation dependent library (CDL) restraints added in 4.0 seconds 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4682 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 75 helices and 19 sheets defined 35.9% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.00 Creating SS restraints... Processing helix chain 'A' and resid 20 through 31 removed outlier: 3.644A pdb=" N GLY A 31 " --> pdb=" O ALA A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 101 removed outlier: 3.681A pdb=" N HIS A 88 " --> pdb=" O ARG A 84 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG A 89 " --> pdb=" O VAL A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 122 removed outlier: 3.930A pdb=" N TYR A 121 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N THR A 122 " --> pdb=" O MET A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 176 Processing helix chain 'A' and resid 184 through 196 Processing helix chain 'A' and resid 223 through 232 removed outlier: 3.536A pdb=" N ALA A 232 " --> pdb=" O ASP A 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 30 removed outlier: 3.890A pdb=" N HIS B 30 " --> pdb=" O GLU B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 101 Processing helix chain 'B' and resid 107 through 122 removed outlier: 3.601A pdb=" N ILE B 117 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR B 121 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N THR B 122 " --> pdb=" O LYS B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 178 Processing helix chain 'B' and resid 186 through 200 Processing helix chain 'B' and resid 230 through 247 Processing helix chain 'C' and resid 17 through 28 removed outlier: 3.733A pdb=" N LYS C 28 " --> pdb=" O GLU C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 59 removed outlier: 3.611A pdb=" N VAL C 59 " --> pdb=" O GLU C 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 56 through 59' Processing helix chain 'C' and resid 77 through 98 Processing helix chain 'C' and resid 104 through 119 removed outlier: 3.937A pdb=" N TYR C 118 " --> pdb=" O LEU C 114 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N THR C 119 " --> pdb=" O LYS C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 175 Processing helix chain 'C' and resid 184 through 197 removed outlier: 3.572A pdb=" N GLU C 197 " --> pdb=" O LYS C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 205 removed outlier: 3.947A pdb=" N ASN C 205 " --> pdb=" O GLY C 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 202 through 205' Processing helix chain 'C' and resid 222 through 240 Processing helix chain 'D' and resid 22 through 33 removed outlier: 4.121A pdb=" N ILE D 31 " --> pdb=" O ALA D 27 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N LYS D 32 " --> pdb=" O ILE D 28 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N LEU D 33 " --> pdb=" O GLU D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 63 No H-bonds generated for 'chain 'D' and resid 61 through 63' Processing helix chain 'D' and resid 84 through 103 removed outlier: 3.858A pdb=" N THR D 87 " --> pdb=" O ASP D 84 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR D 103 " --> pdb=" O TRP D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 120 removed outlier: 3.836A pdb=" N LEU D 119 " --> pdb=" O ALA D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 182 Processing helix chain 'D' and resid 191 through 205 Processing helix chain 'D' and resid 231 through 240 removed outlier: 3.784A pdb=" N ASP D 240 " --> pdb=" O GLU D 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 6 No H-bonds generated for 'chain 'E' and resid 4 through 6' Processing helix chain 'E' and resid 20 through 31 removed outlier: 3.542A pdb=" N ALA E 28 " --> pdb=" O TYR E 24 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N VAL E 29 " --> pdb=" O ALA E 25 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N LYS E 30 " --> pdb=" O MET E 26 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N GLN E 31 " --> pdb=" O GLU E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 99 Processing helix chain 'E' and resid 105 through 120 removed outlier: 4.008A pdb=" N ILE E 118 " --> pdb=" O SER E 114 " (cutoff:3.500A) Proline residue: E 119 - end of helix Processing helix chain 'E' and resid 166 through 174 Processing helix chain 'E' and resid 176 through 178 No H-bonds generated for 'chain 'E' and resid 176 through 178' Processing helix chain 'E' and resid 184 through 198 removed outlier: 3.661A pdb=" N GLU E 197 " --> pdb=" O ARG E 193 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N THR E 198 " --> pdb=" O ALA E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 233 removed outlier: 3.515A pdb=" N VAL E 229 " --> pdb=" O ASP E 226 " (cutoff:3.500A) Proline residue: E 231 - end of helix Processing helix chain 'F' and resid 22 through 31 removed outlier: 3.796A pdb=" N VAL F 31 " --> pdb=" O ALA F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 103 Processing helix chain 'F' and resid 109 through 123 removed outlier: 4.093A pdb=" N TYR F 123 " --> pdb=" O TYR F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 170 through 179 removed outlier: 3.911A pdb=" N LYS F 179 " --> pdb=" O THR F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 184 No H-bonds generated for 'chain 'F' and resid 182 through 184' Processing helix chain 'F' and resid 187 through 200 removed outlier: 4.358A pdb=" N LYS F 192 " --> pdb=" O ARG F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 219 through 221 No H-bonds generated for 'chain 'F' and resid 219 through 221' Processing helix chain 'F' and resid 230 through 243 Processing helix chain 'G' and resid 23 through 34 removed outlier: 3.681A pdb=" N ILE G 32 " --> pdb=" O ALA G 28 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASN G 33 " --> pdb=" O PHE G 29 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLN G 34 " --> pdb=" O LYS G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 65 No H-bonds generated for 'chain 'G' and resid 63 through 65' Processing helix chain 'G' and resid 84 through 105 Processing helix chain 'G' and resid 111 through 126 removed outlier: 3.720A pdb=" N VAL G 124 " --> pdb=" O ASP G 120 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TYR G 125 " --> pdb=" O ILE G 121 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR G 126 " --> pdb=" O SER G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 185 removed outlier: 3.794A pdb=" N LYS G 181 " --> pdb=" O SER G 177 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS G 182 " --> pdb=" O PHE G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 206 Processing helix chain 'G' and resid 232 through 242 Processing helix chain 'H' and resid 64 through 70 Processing helix chain 'H' and resid 73 through 88 removed outlier: 3.726A pdb=" N LEU H 77 " --> pdb=" O LEU H 73 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN H 88 " --> pdb=" O LYS H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 106 Processing helix chain 'I' and resid 35 through 44 Processing helix chain 'I' and resid 62 through 65 No H-bonds generated for 'chain 'I' and resid 62 through 65' Processing helix chain 'I' and resid 77 through 86 Processing helix chain 'I' and resid 146 through 153 Processing helix chain 'I' and resid 172 through 174 No H-bonds generated for 'chain 'I' and resid 172 through 174' Processing helix chain 'I' and resid 181 through 183 No H-bonds generated for 'chain 'I' and resid 181 through 183' Processing helix chain 'I' and resid 214 through 225 Processing helix chain 'I' and resid 244 through 255 removed outlier: 4.180A pdb=" N PHE I 250 " --> pdb=" O THR I 246 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N LYS I 251 " --> pdb=" O VAL I 247 " (cutoff:3.500A) Proline residue: I 252 - end of helix removed outlier: 4.492A pdb=" N SER I 255 " --> pdb=" O LYS I 251 " (cutoff:3.500A) Processing helix chain 'I' and resid 266 through 278 removed outlier: 3.950A pdb=" N THR I 278 " --> pdb=" O LYS I 274 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 39 removed outlier: 4.185A pdb=" N VAL J 27 " --> pdb=" O VAL J 24 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N GLY J 28 " --> pdb=" O GLY J 25 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU J 39 " --> pdb=" O ILE J 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 100 through 113 Processing helix chain 'J' and resid 131 through 135 Processing helix chain 'J' and resid 149 through 158 Processing helix chain 'J' and resid 187 through 197 Processing helix chain 'J' and resid 214 through 228 removed outlier: 3.964A pdb=" N TRP J 227 " --> pdb=" O TYR J 223 " (cutoff:3.500A) Processing helix chain 'K' and resid 98 through 113 Processing helix chain 'K' and resid 119 through 129 Processing helix chain 'L' and resid 73 through 89 removed outlier: 5.950A pdb=" N PHE L 85 " --> pdb=" O ASN L 81 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N VAL L 86 " --> pdb=" O LEU L 82 " (cutoff:3.500A) Processing helix chain 'L' and resid 106 through 118 removed outlier: 3.703A pdb=" N GLU L 114 " --> pdb=" O LYS L 110 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL L 115 " --> pdb=" O ALA L 111 " (cutoff:3.500A) Processing helix chain 'M' and resid 75 through 87 Processing helix chain 'M' and resid 104 through 118 Processing helix chain 'M' and resid 120 through 122 No H-bonds generated for 'chain 'M' and resid 120 through 122' Processing sheet with id= A, first strand: chain 'A' and resid 160 through 163 removed outlier: 4.290A pdb=" N GLY A 43 " --> pdb=" O ALA A 40 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 72 through 78 Processing sheet with id= C, first strand: chain 'B' and resid 161 through 164 Processing sheet with id= D, first strand: chain 'B' and resid 65 through 67 removed outlier: 3.558A pdb=" N LEU B 134 " --> pdb=" O SER B 150 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY B 138 " --> pdb=" O GLN B 146 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY B 157 " --> pdb=" O GLN B 149 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 158 through 161 Processing sheet with id= F, first strand: chain 'C' and resid 62 through 64 removed outlier: 3.513A pdb=" N GLY C 135 " --> pdb=" O ARG C 143 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 167 through 170 Processing sheet with id= H, first strand: chain 'D' and resid 162 through 164 removed outlier: 3.551A pdb=" N ILE D 74 " --> pdb=" O ASP D 71 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N CYS D 76 " --> pdb=" O GLU D 69 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N GLU D 69 " --> pdb=" O CYS D 76 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N MET D 78 " --> pdb=" O ILE D 67 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE D 67 " --> pdb=" O MET D 78 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 158 through 161 Processing sheet with id= J, first strand: chain 'E' and resid 63 through 65 removed outlier: 3.622A pdb=" N LEU E 132 " --> pdb=" O THR E 147 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 163 through 166 removed outlier: 4.042A pdb=" N GLY F 45 " --> pdb=" O CYS F 42 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TRP F 216 " --> pdb=" O GLU F 226 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 67 through 69 Processing sheet with id= M, first strand: chain 'G' and resid 165 through 169 removed outlier: 5.642A pdb=" N THR G 38 " --> pdb=" O GLN G 53 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN G 53 " --> pdb=" O THR G 38 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 161 through 163 removed outlier: 3.615A pdb=" N CYS G 161 " --> pdb=" O LYS G 153 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N VAL G 151 " --> pdb=" O PHE G 163 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY G 148 " --> pdb=" O ASP G 144 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N CYS G 78 " --> pdb=" O LYS G 71 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N LYS G 71 " --> pdb=" O CYS G 78 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N MET G 80 " --> pdb=" O LEU G 69 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU G 69 " --> pdb=" O MET G 80 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'I' and resid 48 through 50 removed outlier: 6.964A pdb=" N PHE I 123 " --> pdb=" O VAL I 96 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N CYS I 98 " --> pdb=" O CYS I 121 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N CYS I 121 " --> pdb=" O CYS I 98 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL I 122 " --> pdb=" O GLN I 136 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N VAL I 132 " --> pdb=" O LEU I 126 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LYS I 70 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N CYS I 135 " --> pdb=" O LYS I 70 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE I 72 " --> pdb=" O CYS I 135 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N CYS I 137 " --> pdb=" O ILE I 72 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ALA I 74 " --> pdb=" O CYS I 137 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N GLN I 163 " --> pdb=" O PHE I 71 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N ILE I 73 " --> pdb=" O GLN I 163 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N THR I 165 " --> pdb=" O ILE I 73 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N ILE I 75 " --> pdb=" O THR I 165 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU I 167 " --> pdb=" O ILE I 75 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'J' and resid 2 through 4 removed outlier: 3.534A pdb=" N SER J 42 " --> pdb=" O SER J 79 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL J 77 " --> pdb=" O ILE J 44 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N TYR J 46 " --> pdb=" O ALA J 75 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N ALA J 75 " --> pdb=" O TYR J 46 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N THR J 16 " --> pdb=" O VAL J 86 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N LEU J 88 " --> pdb=" O THR J 16 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU J 18 " --> pdb=" O LEU J 88 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N LEU J 90 " --> pdb=" O LEU J 18 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ARG J 117 " --> pdb=" O LEU J 17 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N MET J 19 " --> pdb=" O ARG J 117 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ILE J 119 " --> pdb=" O MET J 19 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'K' and resid 150 through 154 removed outlier: 3.576A pdb=" N GLY K 145 " --> pdb=" O HIS K 152 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N CYS K 86 " --> pdb=" O PHE K 79 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N PHE K 79 " --> pdb=" O CYS K 86 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'L' and resid 8 through 16 removed outlier: 4.224A pdb=" N ILE L 8 " --> pdb=" O ALA L 27 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ALA L 94 " --> pdb=" O ILE L 32 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N VAL L 34 " --> pdb=" O ALA L 94 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEU L 96 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N VAL L 36 " --> pdb=" O LEU L 96 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ALA L 98 " --> pdb=" O VAL L 36 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU L 68 " --> pdb=" O LEU L 45 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N SER L 47 " --> pdb=" O VAL L 66 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N VAL L 66 " --> pdb=" O SER L 47 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N GLU L 49 " --> pdb=" O THR L 64 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N THR L 64 " --> pdb=" O GLU L 49 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'M' and resid 13 through 21 removed outlier: 3.626A pdb=" N SER M 36 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLN M 90 " --> pdb=" O LEU M 37 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N LEU M 39 " --> pdb=" O GLN M 90 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N PHE M 92 " --> pdb=" O LEU M 39 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N VAL M 41 " --> pdb=" O PHE M 92 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N SER M 94 " --> pdb=" O VAL M 41 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL M 52 " --> pdb=" O SER M 66 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N SER M 66 " --> pdb=" O VAL M 52 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N MET M 54 " --> pdb=" O SER M 64 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N SER M 64 " --> pdb=" O MET M 54 " (cutoff:3.500A) 868 hydrogen bonds defined for protein. 2445 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: 6.13 Time building geometry restraints manager: 7.76 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: 6323 1.34 - 1.46: 2532 1.46 - 1.57: 10719 1.57 - 1.69: 0 1.69 - 1.81: 174 Bond restraints: 19748 Sorted by residual: bond pdb=" C ACE D 0 " pdb=" O ACE D 0 " ideal model delta sigma weight residual 1.199 1.230 -0.031 2.00e-02 2.50e+03 2.35e+00 bond pdb=" C ACE J 0 " pdb=" O ACE J 0 " ideal model delta sigma weight residual 1.199 1.229 -0.030 2.00e-02 2.50e+03 2.32e+00 bond pdb=" C ACE E 0 " pdb=" O ACE E 0 " ideal model delta sigma weight residual 1.199 1.229 -0.030 2.00e-02 2.50e+03 2.18e+00 bond pdb=" CD GLU M 117 " pdb=" OE1 GLU M 117 " ideal model delta sigma weight residual 1.249 1.230 0.019 1.90e-02 2.77e+03 1.02e+00 bond pdb=" CA ASN K 83 " pdb=" CB ASN K 83 " ideal model delta sigma weight residual 1.530 1.547 -0.017 1.69e-02 3.50e+03 1.01e+00 ... (remaining 19743 not shown) Histogram of bond angle deviations from ideal: 100.11 - 106.88: 488 106.88 - 113.66: 10983 113.66 - 120.44: 7239 120.44 - 127.21: 7832 127.21 - 133.99: 172 Bond angle restraints: 26714 Sorted by residual: angle pdb=" N GLU M 117 " pdb=" CA GLU M 117 " pdb=" CB GLU M 117 " ideal model delta sigma weight residual 110.40 116.35 -5.95 1.63e+00 3.76e-01 1.33e+01 angle pdb=" N THR D 213 " pdb=" CA THR D 213 " pdb=" C THR D 213 " ideal model delta sigma weight residual 114.56 109.94 4.62 1.27e+00 6.20e-01 1.32e+01 angle pdb=" C MET M 116 " pdb=" N GLU M 117 " pdb=" CA GLU M 117 " ideal model delta sigma weight residual 121.14 115.02 6.12 1.75e+00 3.27e-01 1.22e+01 angle pdb=" C PRO K 82 " pdb=" N ASN K 83 " pdb=" CA ASN K 83 " ideal model delta sigma weight residual 121.54 128.10 -6.56 1.91e+00 2.74e-01 1.18e+01 angle pdb=" N GLU C 237 " pdb=" CA GLU C 237 " pdb=" CB GLU C 237 " ideal model delta sigma weight residual 110.28 115.10 -4.82 1.55e+00 4.16e-01 9.68e+00 ... (remaining 26709 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 10885 17.57 - 35.14: 884 35.14 - 52.71: 129 52.71 - 70.28: 36 70.28 - 87.86: 24 Dihedral angle restraints: 11958 sinusoidal: 4710 harmonic: 7248 Sorted by residual: dihedral pdb=" CA TRP F 216 " pdb=" C TRP F 216 " pdb=" N VAL F 217 " pdb=" CA VAL F 217 " ideal model delta harmonic sigma weight residual 180.00 161.07 18.93 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA ASN D 104 " pdb=" C ASN D 104 " pdb=" N GLU D 105 " pdb=" CA GLU D 105 " ideal model delta harmonic sigma weight residual 180.00 161.83 18.17 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA ASP E 94 " pdb=" CB ASP E 94 " pdb=" CG ASP E 94 " pdb=" OD1 ASP E 94 " ideal model delta sinusoidal sigma weight residual -30.00 -87.99 57.99 1 2.00e+01 2.50e-03 1.13e+01 ... (remaining 11955 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1941 0.029 - 0.058: 710 0.058 - 0.088: 211 0.088 - 0.117: 191 0.117 - 0.146: 26 Chirality restraints: 3079 Sorted by residual: chirality pdb=" CA GLU C 237 " pdb=" N GLU C 237 " pdb=" C GLU C 237 " pdb=" CB GLU C 237 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.34e-01 chirality pdb=" CA ILE K 84 " pdb=" N ILE K 84 " pdb=" C ILE K 84 " pdb=" CB ILE K 84 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.81e-01 chirality pdb=" CB THR D 113 " pdb=" CA THR D 113 " pdb=" OG1 THR D 113 " pdb=" CG2 THR D 113 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 4.71e-01 ... (remaining 3076 not shown) Planarity restraints: 3404 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 216 " -0.017 2.00e-02 2.50e+03 1.71e-02 7.28e+00 pdb=" CG TRP F 216 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP F 216 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP F 216 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP F 216 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP F 216 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP F 216 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 216 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 216 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP F 216 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER F 16 " 0.029 5.00e-02 4.00e+02 4.38e-02 3.06e+00 pdb=" N PRO F 17 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO F 17 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO F 17 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO K 82 " 0.008 2.00e-02 2.50e+03 1.65e-02 2.71e+00 pdb=" C PRO K 82 " -0.028 2.00e-02 2.50e+03 pdb=" O PRO K 82 " 0.011 2.00e-02 2.50e+03 pdb=" N ASN K 83 " 0.010 2.00e-02 2.50e+03 ... (remaining 3401 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 3138 2.77 - 3.30: 16952 3.30 - 3.83: 29912 3.83 - 4.37: 34965 4.37 - 4.90: 64667 Nonbonded interactions: 149634 Sorted by model distance: nonbonded pdb=" O ARG K 124 " pdb=" NE2 GLN K 128 " model vdw 2.235 2.520 nonbonded pdb=" OG SER E 33 " pdb=" NZ LYS E 62 " model vdw 2.235 2.520 nonbonded pdb=" OD2 ASP B 151 " pdb=" OG SER B 153 " model vdw 2.239 2.440 nonbonded pdb=" OH TYR I 175 " pdb=" OE1 GLU I 207 " model vdw 2.248 2.440 nonbonded pdb=" OG SER L 29 " pdb=" O PRO M 45 " model vdw 2.259 2.440 ... (remaining 149629 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.010 Normalize map: mean=0, sd=1: 1.900 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: 0.020 Extract box with map and model: 6.870 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 53.730 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 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 : 0.002 0.048 19748 Z= 0.134 Angle : 0.442 10.682 26714 Z= 0.238 Chirality : 0.041 0.146 3079 Planarity : 0.004 0.044 3404 Dihedral : 13.648 87.855 7276 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % 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: 1.76 (0.17), residues: 2456 helix: 2.87 (0.18), residues: 889 sheet: 0.99 (0.23), residues: 550 loop : -0.29 (0.19), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP F 216 HIS 0.003 0.000 HIS D 186 PHE 0.013 0.001 PHE G 9 TYR 0.007 0.001 TYR B 156 ARG 0.002 0.000 ARG H 106 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 285 time to evaluate : 2.289 Fit side-chains REVERT: F 171 GLN cc_start: 0.7521 (tp-100) cc_final: 0.7028 (tp-100) REVERT: M 121 GLU cc_start: 0.7673 (pm20) cc_final: 0.7403 (pm20) outliers start: 0 outliers final: 0 residues processed: 285 average time/residue: 1.5540 time to fit residues: 490.7629 Evaluate side-chains 224 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 2.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 206 optimal weight: 0.8980 chunk 185 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 125 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 192 optimal weight: 0.6980 chunk 74 optimal weight: 4.9990 chunk 116 optimal weight: 6.9990 chunk 142 optimal weight: 7.9990 chunk 222 optimal weight: 10.0000 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN B 84 ASN B 155 ASN ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 ASN G 224 ASN I 280 ASN J 152 GLN J 159 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.0765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 19748 Z= 0.145 Angle : 0.458 10.458 26714 Z= 0.245 Chirality : 0.041 0.151 3079 Planarity : 0.004 0.045 3404 Dihedral : 3.671 17.011 2690 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.14 % Allowed : 7.74 % Favored : 91.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % 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: 1.75 (0.17), residues: 2456 helix: 2.78 (0.18), residues: 887 sheet: 1.29 (0.22), residues: 540 loop : -0.38 (0.19), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP F 216 HIS 0.004 0.001 HIS E 65 PHE 0.010 0.001 PHE M 17 TYR 0.010 0.001 TYR B 136 ARG 0.001 0.000 ARG I 51 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 223 time to evaluate : 2.461 Fit side-chains REVERT: D 1 MET cc_start: 0.8113 (OUTLIER) cc_final: 0.7726 (mmt) REVERT: D 207 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.6649 (mp0) REVERT: F 28 MET cc_start: 0.8734 (mtp) cc_final: 0.8499 (mtm) REVERT: F 102 ASN cc_start: 0.8393 (OUTLIER) cc_final: 0.7721 (m-40) REVERT: F 171 GLN cc_start: 0.7534 (tp-100) cc_final: 0.7031 (tp-100) REVERT: G 112 ASP cc_start: 0.8514 (OUTLIER) cc_final: 0.8117 (p0) REVERT: K 97 MET cc_start: 0.6816 (OUTLIER) cc_final: 0.6445 (ttm) REVERT: K 127 LYS cc_start: 0.8282 (mtpp) cc_final: 0.8010 (ttmt) REVERT: K 128 GLN cc_start: 0.6601 (OUTLIER) cc_final: 0.5741 (mp10) REVERT: M 121 GLU cc_start: 0.7665 (pm20) cc_final: 0.7389 (pm20) outliers start: 24 outliers final: 7 residues processed: 234 average time/residue: 1.5356 time to fit residues: 400.9834 Evaluate side-chains 224 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 211 time to evaluate : 2.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 228 MET Chi-restraints excluded: chain F residue 102 ASN Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain K residue 97 MET Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 128 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 123 optimal weight: 0.7980 chunk 69 optimal weight: 0.4980 chunk 185 optimal weight: 3.9990 chunk 151 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 222 optimal weight: 8.9990 chunk 240 optimal weight: 0.4980 chunk 198 optimal weight: 0.9980 chunk 221 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 chunk 178 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 ASN B 88 ASN B 155 ASN ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 224 ASN I 280 ASN J 159 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.0928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 19748 Z= 0.117 Angle : 0.420 10.896 26714 Z= 0.225 Chirality : 0.040 0.139 3079 Planarity : 0.004 0.043 3404 Dihedral : 3.554 17.056 2690 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.19 % Allowed : 9.07 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % 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 (0.17), residues: 2456 helix: 2.73 (0.18), residues: 890 sheet: 1.31 (0.22), residues: 542 loop : -0.31 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 216 HIS 0.003 0.000 HIS E 65 PHE 0.010 0.001 PHE M 17 TYR 0.008 0.001 TYR J 223 ARG 0.002 0.000 ARG D 10 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 216 time to evaluate : 2.266 Fit side-chains REVERT: D 207 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.6522 (mp0) REVERT: E 203 GLN cc_start: 0.7889 (OUTLIER) cc_final: 0.7556 (mt0) REVERT: F 28 MET cc_start: 0.8694 (mtp) cc_final: 0.8450 (mtm) REVERT: F 171 GLN cc_start: 0.7503 (tp-100) cc_final: 0.7056 (tp-100) REVERT: G 112 ASP cc_start: 0.8443 (OUTLIER) cc_final: 0.8028 (p0) REVERT: H 80 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.8036 (tt0) REVERT: H 81 MET cc_start: 0.8250 (OUTLIER) cc_final: 0.7979 (mtp) REVERT: K 128 GLN cc_start: 0.6607 (OUTLIER) cc_final: 0.5765 (mp10) REVERT: M 121 GLU cc_start: 0.7690 (pm20) cc_final: 0.7442 (pm20) outliers start: 25 outliers final: 8 residues processed: 227 average time/residue: 1.5275 time to fit residues: 386.1095 Evaluate side-chains 219 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 205 time to evaluate : 2.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain E residue 203 GLN Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain H residue 80 GLN Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 128 GLN Chi-restraints excluded: chain M residue 54 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 220 optimal weight: 10.0000 chunk 167 optimal weight: 10.0000 chunk 115 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 106 optimal weight: 7.9990 chunk 149 optimal weight: 4.9990 chunk 223 optimal weight: 4.9990 chunk 236 optimal weight: 10.0000 chunk 116 optimal weight: 9.9990 chunk 212 optimal weight: 0.0000 chunk 63 optimal weight: 5.9990 overall best weight: 3.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN B 69 ASN ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 GLN G 224 ASN I 103 ASN J 159 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 19748 Z= 0.341 Angle : 0.564 9.887 26714 Z= 0.299 Chirality : 0.045 0.183 3079 Planarity : 0.005 0.047 3404 Dihedral : 4.224 21.859 2690 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.57 % Allowed : 10.68 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % 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: 1.33 (0.17), residues: 2456 helix: 2.38 (0.18), residues: 880 sheet: 1.17 (0.22), residues: 536 loop : -0.62 (0.18), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 216 HIS 0.006 0.001 HIS E 65 PHE 0.014 0.002 PHE E 97 TYR 0.014 0.002 TYR B 136 ARG 0.003 0.000 ARG A 84 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 211 time to evaluate : 2.415 Fit side-chains REVERT: C 23 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.8165 (mt0) REVERT: D 1 MET cc_start: 0.8995 (mmt) cc_final: 0.8130 (mmt) REVERT: D 148 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7426 (pm20) REVERT: D 207 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.6411 (mp0) REVERT: F 171 GLN cc_start: 0.7696 (tp-100) cc_final: 0.7207 (tp-100) REVERT: G 112 ASP cc_start: 0.8650 (OUTLIER) cc_final: 0.8274 (p0) REVERT: G 130 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7234 (mp0) REVERT: H 80 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.7995 (tt0) REVERT: K 128 GLN cc_start: 0.6714 (OUTLIER) cc_final: 0.5835 (mp10) REVERT: M 121 GLU cc_start: 0.7749 (pm20) cc_final: 0.7423 (pm20) outliers start: 33 outliers final: 13 residues processed: 228 average time/residue: 1.5669 time to fit residues: 398.2448 Evaluate side-chains 222 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 202 time to evaluate : 2.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 148 GLU Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain E residue 227 ASP Chi-restraints excluded: chain G residue 90 GLN Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain H residue 80 GLN Chi-restraints excluded: chain J residue 55 MET Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain K residue 97 MET Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 128 GLN Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain M residue 54 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 197 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 176 optimal weight: 0.9990 chunk 97 optimal weight: 0.6980 chunk 202 optimal weight: 0.9980 chunk 163 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 120 optimal weight: 4.9990 chunk 212 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN A 214 ASN ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN F 181 GLN G 224 ASN I 103 ASN J 159 ASN ** K 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 19748 Z= 0.137 Angle : 0.440 10.406 26714 Z= 0.237 Chirality : 0.041 0.146 3079 Planarity : 0.004 0.046 3404 Dihedral : 3.821 18.378 2690 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.23 % Allowed : 12.44 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % 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: 1.57 (0.17), residues: 2456 helix: 2.55 (0.18), residues: 880 sheet: 1.30 (0.22), residues: 532 loop : -0.43 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 216 HIS 0.004 0.001 HIS E 65 PHE 0.009 0.001 PHE M 17 TYR 0.008 0.001 TYR B 136 ARG 0.002 0.000 ARG F 224 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 209 time to evaluate : 2.381 Fit side-chains REVERT: D 207 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.6478 (mp0) REVERT: F 28 MET cc_start: 0.8719 (mtp) cc_final: 0.8467 (mtm) REVERT: F 171 GLN cc_start: 0.7603 (tp-100) cc_final: 0.7113 (tp-100) REVERT: G 112 ASP cc_start: 0.8541 (OUTLIER) cc_final: 0.8156 (p0) REVERT: H 80 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.8011 (tt0) REVERT: K 128 GLN cc_start: 0.6590 (OUTLIER) cc_final: 0.5729 (mp10) REVERT: M 121 GLU cc_start: 0.7780 (pm20) cc_final: 0.7468 (pm20) outliers start: 26 outliers final: 11 residues processed: 222 average time/residue: 1.5924 time to fit residues: 392.5205 Evaluate side-chains 214 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 199 time to evaluate : 2.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain E residue 227 ASP Chi-restraints excluded: chain G residue 90 GLN Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain H residue 80 GLN Chi-restraints excluded: chain J residue 55 MET Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 128 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 79 optimal weight: 0.9980 chunk 213 optimal weight: 8.9990 chunk 46 optimal weight: 0.9980 chunk 139 optimal weight: 7.9990 chunk 58 optimal weight: 0.9980 chunk 237 optimal weight: 6.9990 chunk 196 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 19 optimal weight: 7.9990 chunk 78 optimal weight: 6.9990 chunk 124 optimal weight: 7.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN B 146 GLN G 224 ASN J 159 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19748 Z= 0.233 Angle : 0.499 10.100 26714 Z= 0.265 Chirality : 0.043 0.162 3079 Planarity : 0.004 0.048 3404 Dihedral : 3.990 19.962 2690 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.80 % Allowed : 12.58 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % 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: 1.44 (0.17), residues: 2456 helix: 2.45 (0.18), residues: 881 sheet: 1.26 (0.22), residues: 532 loop : -0.54 (0.18), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 149 HIS 0.005 0.001 HIS E 65 PHE 0.011 0.001 PHE E 97 TYR 0.012 0.001 TYR B 136 ARG 0.002 0.000 ARG F 233 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 206 time to evaluate : 2.246 Fit side-chains REVERT: D 148 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7413 (pm20) REVERT: D 207 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.6366 (mp0) REVERT: E 203 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.7582 (mt0) REVERT: F 28 MET cc_start: 0.8770 (mtp) cc_final: 0.8490 (mtm) REVERT: F 171 GLN cc_start: 0.7694 (tp-100) cc_final: 0.7171 (tp-100) REVERT: G 112 ASP cc_start: 0.8584 (OUTLIER) cc_final: 0.8208 (p0) REVERT: H 80 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.8001 (tt0) REVERT: H 110 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7902 (mt-10) REVERT: I 283 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.8529 (mt0) REVERT: J 19 MET cc_start: 0.8710 (OUTLIER) cc_final: 0.8158 (ttt) REVERT: K 97 MET cc_start: 0.6786 (OUTLIER) cc_final: 0.6360 (ttm) REVERT: K 128 GLN cc_start: 0.6664 (OUTLIER) cc_final: 0.5786 (mp10) REVERT: M 121 GLU cc_start: 0.7793 (pm20) cc_final: 0.7470 (pm20) outliers start: 38 outliers final: 14 residues processed: 226 average time/residue: 1.5873 time to fit residues: 397.6311 Evaluate side-chains 225 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 201 time to evaluate : 2.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 148 GLU Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain E residue 203 GLN Chi-restraints excluded: chain G residue 90 GLN Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain G residue 146 GLU Chi-restraints excluded: chain H residue 80 GLN Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain I residue 283 GLN Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 19 MET Chi-restraints excluded: chain J residue 55 MET Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain K residue 97 MET Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 128 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 228 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 135 optimal weight: 3.9990 chunk 173 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 199 optimal weight: 9.9990 chunk 132 optimal weight: 0.2980 chunk 236 optimal weight: 2.9990 chunk 147 optimal weight: 0.0470 chunk 143 optimal weight: 2.9990 chunk 109 optimal weight: 8.9990 overall best weight: 1.8684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN A 214 ASN B 146 GLN G 224 ASN J 159 ASN ** K 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19748 Z= 0.204 Angle : 0.480 9.872 26714 Z= 0.257 Chirality : 0.042 0.153 3079 Planarity : 0.004 0.047 3404 Dihedral : 3.976 20.030 2690 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.52 % Allowed : 13.25 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % 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: 1.45 (0.17), residues: 2456 helix: 2.43 (0.18), residues: 879 sheet: 1.30 (0.22), residues: 531 loop : -0.53 (0.18), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 149 HIS 0.004 0.001 HIS E 65 PHE 0.009 0.001 PHE M 17 TYR 0.011 0.001 TYR B 136 ARG 0.002 0.000 ARG F 233 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 206 time to evaluate : 2.336 Fit side-chains REVERT: D 207 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.6422 (mp0) REVERT: E 203 GLN cc_start: 0.7913 (OUTLIER) cc_final: 0.7584 (mt0) REVERT: F 28 MET cc_start: 0.8769 (mtp) cc_final: 0.8493 (mtm) REVERT: F 171 GLN cc_start: 0.7675 (tp-100) cc_final: 0.7153 (tp-100) REVERT: G 112 ASP cc_start: 0.8608 (OUTLIER) cc_final: 0.8234 (p0) REVERT: H 80 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.7997 (tt0) REVERT: H 110 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7841 (mt-10) REVERT: K 97 MET cc_start: 0.6787 (OUTLIER) cc_final: 0.6357 (ttm) REVERT: K 128 GLN cc_start: 0.6606 (OUTLIER) cc_final: 0.5712 (mp10) REVERT: M 117 GLU cc_start: 0.7007 (OUTLIER) cc_final: 0.6700 (mp0) REVERT: M 121 GLU cc_start: 0.7812 (pm20) cc_final: 0.7499 (pm20) outliers start: 32 outliers final: 16 residues processed: 223 average time/residue: 1.6200 time to fit residues: 399.8373 Evaluate side-chains 223 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 199 time to evaluate : 2.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 203 GLN Chi-restraints excluded: chain F residue 102 ASN Chi-restraints excluded: chain G residue 90 GLN Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 80 GLN Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 55 MET Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain K residue 97 MET Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 128 GLN Chi-restraints excluded: chain M residue 54 MET Chi-restraints excluded: chain M residue 117 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 146 optimal weight: 7.9990 chunk 94 optimal weight: 3.9990 chunk 141 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 150 optimal weight: 4.9990 chunk 160 optimal weight: 0.7980 chunk 116 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 185 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN A 214 ASN B 146 GLN F 64 ASN G 224 ASN J 159 ASN ** K 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 19748 Z= 0.132 Angle : 0.451 10.215 26714 Z= 0.241 Chirality : 0.041 0.144 3079 Planarity : 0.004 0.046 3404 Dihedral : 3.780 17.935 2690 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.71 % Allowed : 13.44 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % 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: 1.61 (0.17), residues: 2456 helix: 2.58 (0.18), residues: 878 sheet: 1.36 (0.22), residues: 532 loop : -0.42 (0.18), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 149 HIS 0.003 0.001 HIS E 65 PHE 0.009 0.001 PHE M 17 TYR 0.009 0.001 TYR B 136 ARG 0.002 0.000 ARG H 106 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 204 time to evaluate : 2.389 Fit side-chains REVERT: D 207 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.6429 (mp0) REVERT: E 203 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7571 (mt0) REVERT: F 28 MET cc_start: 0.8725 (mtp) cc_final: 0.8439 (mtm) REVERT: F 171 GLN cc_start: 0.7614 (tp-100) cc_final: 0.7094 (tp-100) REVERT: G 112 ASP cc_start: 0.8537 (OUTLIER) cc_final: 0.8158 (p0) REVERT: H 80 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.8018 (tt0) REVERT: H 110 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7810 (mt-10) REVERT: I 283 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.8530 (mt0) REVERT: J 19 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.7771 (ttt) REVERT: K 97 MET cc_start: 0.6727 (OUTLIER) cc_final: 0.6260 (ttm) REVERT: K 128 GLN cc_start: 0.6579 (OUTLIER) cc_final: 0.5694 (mp10) REVERT: M 117 GLU cc_start: 0.6946 (OUTLIER) cc_final: 0.6631 (mp0) REVERT: M 121 GLU cc_start: 0.7806 (pm20) cc_final: 0.7494 (pm20) outliers start: 36 outliers final: 16 residues processed: 222 average time/residue: 1.6295 time to fit residues: 400.5170 Evaluate side-chains 225 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 199 time to evaluate : 2.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 133 MET Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain E residue 203 GLN Chi-restraints excluded: chain G residue 90 GLN Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 80 GLN Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 99 ASN Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain I residue 283 GLN Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 19 MET Chi-restraints excluded: chain J residue 55 MET Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain K residue 97 MET Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 128 GLN Chi-restraints excluded: chain M residue 54 MET Chi-restraints excluded: chain M residue 117 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 214 optimal weight: 5.9990 chunk 226 optimal weight: 3.9990 chunk 206 optimal weight: 2.9990 chunk 220 optimal weight: 0.0570 chunk 132 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 172 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 198 optimal weight: 6.9990 chunk 208 optimal weight: 5.9990 chunk 219 optimal weight: 4.9990 overall best weight: 1.5902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN B 146 GLN G 224 ASN J 159 ASN ** K 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19748 Z= 0.184 Angle : 0.475 9.800 26714 Z= 0.254 Chirality : 0.042 0.150 3079 Planarity : 0.004 0.047 3404 Dihedral : 3.864 18.278 2690 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.52 % Allowed : 13.68 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % 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: 1.55 (0.17), residues: 2456 helix: 2.53 (0.18), residues: 879 sheet: 1.35 (0.22), residues: 532 loop : -0.48 (0.18), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 149 HIS 0.004 0.001 HIS E 65 PHE 0.009 0.001 PHE E 97 TYR 0.011 0.001 TYR B 136 ARG 0.003 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 199 time to evaluate : 2.500 Fit side-chains REVERT: C 23 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.8234 (mt0) REVERT: D 207 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.6391 (mp0) REVERT: E 203 GLN cc_start: 0.7908 (OUTLIER) cc_final: 0.7578 (mt0) REVERT: F 28 MET cc_start: 0.8750 (mtp) cc_final: 0.8454 (mtm) REVERT: F 171 GLN cc_start: 0.7664 (tp-100) cc_final: 0.7133 (tp-100) REVERT: G 112 ASP cc_start: 0.8549 (OUTLIER) cc_final: 0.8161 (p0) REVERT: H 80 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7974 (tt0) REVERT: H 81 MET cc_start: 0.8326 (OUTLIER) cc_final: 0.8051 (mtp) REVERT: H 110 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7752 (mt-10) REVERT: I 283 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.8535 (mt0) REVERT: J 19 MET cc_start: 0.8584 (OUTLIER) cc_final: 0.7811 (ttt) REVERT: K 97 MET cc_start: 0.6777 (OUTLIER) cc_final: 0.6348 (ttm) REVERT: K 128 GLN cc_start: 0.6625 (OUTLIER) cc_final: 0.5708 (mp10) REVERT: M 117 GLU cc_start: 0.7012 (OUTLIER) cc_final: 0.6677 (mp0) REVERT: M 121 GLU cc_start: 0.7791 (pm20) cc_final: 0.7532 (pm20) outliers start: 32 outliers final: 15 residues processed: 219 average time/residue: 1.6377 time to fit residues: 397.3191 Evaluate side-chains 223 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 196 time to evaluate : 2.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 203 GLN Chi-restraints excluded: chain G residue 90 GLN Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain H residue 80 GLN Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain I residue 283 GLN Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 19 MET Chi-restraints excluded: chain J residue 55 MET Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain K residue 97 MET Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 128 GLN Chi-restraints excluded: chain M residue 54 MET Chi-restraints excluded: chain M residue 117 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 144 optimal weight: 6.9990 chunk 232 optimal weight: 9.9990 chunk 142 optimal weight: 3.9990 chunk 110 optimal weight: 8.9990 chunk 161 optimal weight: 3.9990 chunk 244 optimal weight: 4.9990 chunk 224 optimal weight: 0.9980 chunk 194 optimal weight: 0.9990 chunk 20 optimal weight: 0.0050 chunk 150 optimal weight: 0.9980 chunk 119 optimal weight: 9.9990 overall best weight: 1.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN A 214 ASN B 146 GLN ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 181 GLN G 224 ASN J 159 ASN ** K 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19748 Z= 0.168 Angle : 0.470 9.974 26714 Z= 0.250 Chirality : 0.041 0.143 3079 Planarity : 0.004 0.047 3404 Dihedral : 3.838 18.125 2690 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.57 % Allowed : 13.77 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % 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: 1.58 (0.17), residues: 2456 helix: 2.55 (0.18), residues: 879 sheet: 1.36 (0.22), residues: 532 loop : -0.45 (0.18), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 149 HIS 0.004 0.001 HIS E 65 PHE 0.009 0.001 PHE M 17 TYR 0.010 0.001 TYR B 136 ARG 0.002 0.000 ARG H 106 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 200 time to evaluate : 2.477 Fit side-chains REVERT: C 23 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.8251 (mt0) REVERT: D 207 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.6408 (mp0) REVERT: E 203 GLN cc_start: 0.7903 (OUTLIER) cc_final: 0.7568 (mt0) REVERT: F 28 MET cc_start: 0.8724 (mtp) cc_final: 0.8432 (mtm) REVERT: F 171 GLN cc_start: 0.7646 (tp-100) cc_final: 0.7119 (tp-100) REVERT: G 112 ASP cc_start: 0.8568 (OUTLIER) cc_final: 0.8208 (p0) REVERT: H 110 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7704 (mt-10) REVERT: I 283 GLN cc_start: 0.8806 (OUTLIER) cc_final: 0.8538 (mt0) REVERT: J 19 MET cc_start: 0.8563 (OUTLIER) cc_final: 0.7781 (ttt) REVERT: K 97 MET cc_start: 0.6773 (OUTLIER) cc_final: 0.6308 (ttm) REVERT: K 128 GLN cc_start: 0.6599 (OUTLIER) cc_final: 0.5690 (mp10) REVERT: M 117 GLU cc_start: 0.7009 (OUTLIER) cc_final: 0.6672 (mp0) REVERT: M 121 GLU cc_start: 0.7792 (pm20) cc_final: 0.7537 (pm20) outliers start: 33 outliers final: 16 residues processed: 220 average time/residue: 1.6577 time to fit residues: 402.8832 Evaluate side-chains 222 residues out of total 2149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 196 time to evaluate : 2.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 133 MET Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain E residue 203 GLN Chi-restraints excluded: chain G residue 90 GLN Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain I residue 195 GLN Chi-restraints excluded: chain I residue 283 GLN Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 19 MET Chi-restraints excluded: chain J residue 55 MET Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain K residue 97 MET Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 128 GLN Chi-restraints excluded: chain M residue 54 MET Chi-restraints excluded: chain M residue 117 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 154 optimal weight: 0.9980 chunk 207 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 179 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 54 optimal weight: 9.9990 chunk 194 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 199 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN A 214 ASN B 146 GLN G 224 ASN J 159 ASN ** K 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.109531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.080617 restraints weight = 30419.902| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 2.35 r_work: 0.2881 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19748 Z= 0.248 Angle : 0.517 9.595 26714 Z= 0.275 Chirality : 0.043 0.165 3079 Planarity : 0.004 0.048 3404 Dihedral : 4.053 19.798 2690 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.42 % Allowed : 13.91 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % 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: 1.42 (0.17), residues: 2456 helix: 2.42 (0.18), residues: 880 sheet: 1.29 (0.22), residues: 536 loop : -0.57 (0.18), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 149 HIS 0.005 0.001 HIS E 65 PHE 0.011 0.001 PHE E 97 TYR 0.014 0.001 TYR B 136 ARG 0.003 0.000 ARG F 233 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7164.91 seconds wall clock time: 129 minutes 6.94 seconds (7746.94 seconds total)