Starting phenix.real_space_refine on Thu Feb 15 19:59:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7egf_31115/02_2024/7egf_31115.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7egf_31115/02_2024/7egf_31115.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7egf_31115/02_2024/7egf_31115.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7egf_31115/02_2024/7egf_31115.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7egf_31115/02_2024/7egf_31115.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7egf_31115/02_2024/7egf_31115.pdb" } resolution = 3.16 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= 0.002 sd= 0.065 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 69 5.16 5 C 8448 2.51 5 N 2316 2.21 5 O 2470 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "P GLU 286": "OE1" <-> "OE2" Residue "P GLU 320": "OE1" <-> "OE2" Residue "d GLU 847": "OE1" <-> "OE2" Residue "d ARG 851": "NH1" <-> "NH2" Residue "d GLU 858": "OE1" <-> "OE2" Residue "d ARG 865": "NH1" <-> "NH2" Residue "d GLU 870": "OE1" <-> "OE2" Residue "d ARG 881": "NH1" <-> "NH2" Residue "d ARG 909": "NH1" <-> "NH2" Residue "d GLU 954": "OE1" <-> "OE2" Residue "d GLU 962": "OE1" <-> "OE2" Residue "d ARG 1057": "NH1" <-> "NH2" Residue "e TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 235": "OE1" <-> "OE2" Residue "e GLU 250": "OE1" <-> "OE2" Residue "e GLU 257": "OE1" <-> "OE2" Residue "e GLU 335": "OE1" <-> "OE2" Residue "e ARG 365": "NH1" <-> "NH2" Residue "e ARG 450": "NH1" <-> "NH2" Residue "e ARG 452": "NH1" <-> "NH2" Residue "e ARG 607": "NH1" <-> "NH2" Residue "e ARG 634": "NH1" <-> "NH2" Residue "e GLU 706": "OE1" <-> "OE2" Residue "f GLU 17": "OE1" <-> "OE2" Residue "f ARG 63": "NH1" <-> "NH2" Residue "f PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 109": "OE1" <-> "OE2" Residue "i ARG 34": "NH1" <-> "NH2" Residue "i GLU 41": "OE1" <-> "OE2" Residue "i ARG 78": "NH1" <-> "NH2" Residue "i ARG 119": "NH1" <-> "NH2" Residue "j GLU 145": "OE1" <-> "OE2" Residue "k ARG 126": "NH1" <-> "NH2" Residue "k GLU 167": "OE1" <-> "OE2" Residue "k GLU 174": "OE1" <-> "OE2" Residue "k ARG 192": "NH1" <-> "NH2" Residue "k ARG 193": "NH1" <-> "NH2" Residue "l ARG 104": "NH1" <-> "NH2" Residue "l GLU 112": "OE1" <-> "OE2" Residue "l GLU 121": "OE1" <-> "OE2" Residue "m ARG 30": "NH1" <-> "NH2" Residue "m ASP 45": "OD1" <-> "OD2" Residue "m PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 91": "NH1" <-> "NH2" Residue "m ARG 114": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13303 Number of models: 1 Model: "" Number of chains: 10 Chain: "P" Number of atoms: 1412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1412 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 9, 'TRANS': 167} Chain: "c" Number of atoms: 1011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1011 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 118} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "d" Number of atoms: 1307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1307 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 155} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "e" Number of atoms: 4327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4327 Classifications: {'peptide': 539} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 516} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "f" Number of atoms: 1135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1135 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 11, 'TRANS': 131} Chain: "i" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 967 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 108} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "j" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 759 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 6, 'TRANS': 88} Chain breaks: 1 Chain: "k" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 785 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "l" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 876 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 3, 'TRANS': 103} Chain: "m" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 724 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Time building chain proxies: 6.67, per 1000 atoms: 0.50 Number of scatterers: 13303 At special positions: 0 Unit cell: (103.39, 138.205, 136.095, 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 69 16.00 O 2470 8.00 N 2316 7.00 C 8448 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: 4.55 Conformation dependent library (CDL) restraints added in 2.2 seconds 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3146 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 14 sheets defined 44.9% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'P' and resid 179 through 187 removed outlier: 4.049A pdb=" N ILE P 183 " --> pdb=" O ASP P 179 " (cutoff:3.500A) Processing helix chain 'P' and resid 226 through 243 Processing helix chain 'P' and resid 269 through 277 removed outlier: 3.834A pdb=" N LEU P 273 " --> pdb=" O ARG P 269 " (cutoff:3.500A) Processing helix chain 'P' and resid 317 through 335 removed outlier: 3.972A pdb=" N ILE P 321 " --> pdb=" O VAL P 317 " (cutoff:3.500A) Proline residue: P 330 - end of helix Processing helix chain 'c' and resid 2 through 16 Processing helix chain 'c' and resid 16 through 21 removed outlier: 3.552A pdb=" N ALA c 20 " --> pdb=" O GLN c 16 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU c 21 " --> pdb=" O ILE c 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 16 through 21' Processing helix chain 'c' and resid 28 through 56 removed outlier: 3.562A pdb=" N HIS c 32 " --> pdb=" O LEU c 28 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU c 33 " --> pdb=" O SER c 29 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU c 34 " --> pdb=" O ALA c 30 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP c 36 " --> pdb=" O HIS c 32 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN c 43 " --> pdb=" O GLN c 39 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER c 53 " --> pdb=" O CYS c 49 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N TYR c 56 " --> pdb=" O TYR c 52 " (cutoff:3.500A) Processing helix chain 'c' and resid 62 through 74 removed outlier: 3.935A pdb=" N GLN c 71 " --> pdb=" O GLY c 67 " (cutoff:3.500A) Processing helix chain 'c' and resid 76 through 87 removed outlier: 3.607A pdb=" N GLU c 81 " --> pdb=" O LEU c 77 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP c 82 " --> pdb=" O HIS c 78 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN c 86 " --> pdb=" O ASP c 82 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE c 87 " --> pdb=" O TYR c 83 " (cutoff:3.500A) Processing helix chain 'd' and resid 844 through 849 removed outlier: 3.515A pdb=" N GLU d 848 " --> pdb=" O ASN d 844 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER d 849 " --> pdb=" O LEU d 845 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 844 through 849' Processing helix chain 'd' and resid 849 through 855 removed outlier: 4.155A pdb=" N LEU d 853 " --> pdb=" O SER d 849 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N THR d 855 " --> pdb=" O ARG d 851 " (cutoff:3.500A) Processing helix chain 'd' and resid 856 through 858 No H-bonds generated for 'chain 'd' and resid 856 through 858' Processing helix chain 'd' and resid 874 through 885 removed outlier: 3.676A pdb=" N ARG d 880 " --> pdb=" O ALA d 876 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU d 883 " --> pdb=" O GLN d 879 " (cutoff:3.500A) Processing helix chain 'd' and resid 898 through 922 removed outlier: 3.548A pdb=" N HIS d 904 " --> pdb=" O SER d 900 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN d 907 " --> pdb=" O SER d 903 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU d 913 " --> pdb=" O ARG d 909 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU d 919 " --> pdb=" O GLU d 915 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR d 920 " --> pdb=" O LYS d 916 " (cutoff:3.500A) Processing helix chain 'd' and resid 923 through 926 Processing helix chain 'd' and resid 939 through 968 Processing helix chain 'd' and resid 1059 through 1069 removed outlier: 3.754A pdb=" N LEU d1063 " --> pdb=" O ASN d1059 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N CYS d1066 " --> pdb=" O ASP d1062 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN d1069 " --> pdb=" O PHE d1065 " (cutoff:3.500A) Processing helix chain 'd' and resid 1076 through 1083 removed outlier: 3.688A pdb=" N TYR d1080 " --> pdb=" O SER d1076 " (cutoff:3.500A) Processing helix chain 'e' and resid 213 through 228 Processing helix chain 'e' and resid 229 through 255 removed outlier: 4.511A pdb=" N ALA e 234 " --> pdb=" O ASP e 230 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU e 235 " --> pdb=" O CYS e 231 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLN e 238 " --> pdb=" O ALA e 234 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N LEU e 239 " --> pdb=" O GLU e 235 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N PHE e 240 " --> pdb=" O LEU e 236 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N TYR e 241 " --> pdb=" O SER e 237 " (cutoff:3.500A) Proline residue: e 242 - end of helix Processing helix chain 'e' and resid 256 through 268 Processing helix chain 'e' and resid 276 through 285 Processing helix chain 'e' and resid 287 through 292 removed outlier: 3.906A pdb=" N MET e 291 " --> pdb=" O LYS e 287 " (cutoff:3.500A) Processing helix chain 'e' and resid 310 through 322 removed outlier: 3.604A pdb=" N GLN e 315 " --> pdb=" O ARG e 311 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LEU e 316 " --> pdb=" O ASP e 312 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU e 317 " --> pdb=" O SER e 313 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN e 322 " --> pdb=" O LYS e 318 " (cutoff:3.500A) Processing helix chain 'e' and resid 329 through 334 removed outlier: 3.926A pdb=" N VAL e 333 " --> pdb=" O ILE e 329 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN e 334 " --> pdb=" O TRP e 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 329 through 334' Processing helix chain 'e' and resid 433 through 449 Processing helix chain 'e' and resid 509 through 516 Processing helix chain 'e' and resid 522 through 527 Processing helix chain 'f' and resid 16 through 27 removed outlier: 3.719A pdb=" N LYS f 20 " --> pdb=" O SER f 16 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL f 21 " --> pdb=" O GLU f 17 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL f 22 " --> pdb=" O SER f 18 " (cutoff:3.500A) Processing helix chain 'f' and resid 32 through 61 removed outlier: 3.535A pdb=" N ASP f 41 " --> pdb=" O GLN f 37 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLU f 42 " --> pdb=" O LEU f 38 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR f 45 " --> pdb=" O ASP f 41 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS f 48 " --> pdb=" O SER f 44 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP f 53 " --> pdb=" O GLU f 49 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS f 56 " --> pdb=" O GLN f 52 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE f 57 " --> pdb=" O ASP f 53 " (cutoff:3.500A) Processing helix chain 'f' and resid 67 through 76 removed outlier: 4.017A pdb=" N ILE f 71 " --> pdb=" O THR f 67 " (cutoff:3.500A) Processing helix chain 'f' and resid 114 through 119 Processing helix chain 'i' and resid 18 through 26 Processing helix chain 'i' and resid 33 through 61 removed outlier: 4.306A pdb=" N ASN i 37 " --> pdb=" O PRO i 33 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU i 41 " --> pdb=" O ASN i 37 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA i 43 " --> pdb=" O MET i 39 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL i 47 " --> pdb=" O ALA i 43 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASP i 52 " --> pdb=" O THR i 48 " (cutoff:3.500A) Processing helix chain 'i' and resid 67 through 77 removed outlier: 3.511A pdb=" N VAL i 71 " --> pdb=" O ASP i 67 " (cutoff:3.500A) Processing helix chain 'i' and resid 88 through 100 removed outlier: 3.967A pdb=" N ASP i 94 " --> pdb=" O ASP i 90 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN i 98 " --> pdb=" O ASP i 94 " (cutoff:3.500A) Processing helix chain 'j' and resid 115 through 124 Processing helix chain 'j' and resid 131 through 139 Processing helix chain 'j' and resid 148 through 177 removed outlier: 3.939A pdb=" N ILE j 152 " --> pdb=" O ASP j 148 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG j 153 " --> pdb=" O PRO j 149 " (cutoff:3.500A) Processing helix chain 'j' and resid 196 through 205 Proline residue: j 202 - end of helix removed outlier: 3.571A pdb=" N SER j 205 " --> pdb=" O THR j 201 " (cutoff:3.500A) Processing helix chain 'k' and resid 116 through 127 removed outlier: 3.503A pdb=" N ARG k 125 " --> pdb=" O TYR k 121 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER k 127 " --> pdb=" O MET k 123 " (cutoff:3.500A) Processing helix chain 'k' and resid 130 through 143 removed outlier: 4.102A pdb=" N ARG k 136 " --> pdb=" O ALA k 132 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE k 141 " --> pdb=" O LEU k 137 " (cutoff:3.500A) Processing helix chain 'k' and resid 147 through 176 removed outlier: 3.608A pdb=" N ALA k 153 " --> pdb=" O ASN k 149 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER k 158 " --> pdb=" O MET k 154 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS k 159 " --> pdb=" O SER k 155 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU k 167 " --> pdb=" O GLY k 163 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU k 168 " --> pdb=" O GLU k 164 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP k 171 " --> pdb=" O GLU k 167 " (cutoff:3.500A) Processing helix chain 'k' and resid 184 through 197 removed outlier: 3.609A pdb=" N LYS k 197 " --> pdb=" O ARG k 193 " (cutoff:3.500A) Processing helix chain 'l' and resid 61 through 69 Processing helix chain 'l' and resid 77 through 106 Processing helix chain 'l' and resid 113 through 123 removed outlier: 3.743A pdb=" N LEU l 118 " --> pdb=" O LYS l 114 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N HIS l 119 " --> pdb=" O ASP l 115 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU l 120 " --> pdb=" O VAL l 116 " (cutoff:3.500A) Processing helix chain 'l' and resid 145 through 161 removed outlier: 3.794A pdb=" N ALA l 153 " --> pdb=" O LYS l 149 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU l 154 " --> pdb=" O GLN l 150 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE l 155 " --> pdb=" O ARG l 151 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG l 156 " --> pdb=" O MET l 152 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LYS l 157 " --> pdb=" O ALA l 153 " (cutoff:3.500A) Processing helix chain 'm' and resid 34 through 43 removed outlier: 3.733A pdb=" N CYS m 38 " --> pdb=" O LYS m 34 " (cutoff:3.500A) Processing helix chain 'm' and resid 50 through 75 Processing helix chain 'm' and resid 82 through 91 Processing helix chain 'm' and resid 93 through 114 Processing sheet with id=AA1, first strand: chain 'P' and resid 190 through 193 removed outlier: 4.404A pdb=" N ASN P 193 " --> pdb=" O ALA P 199 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ALA P 199 " --> pdb=" O ASN P 193 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N THR P 209 " --> pdb=" O ILE P 204 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY P 223 " --> pdb=" O ILE P 168 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N ILE P 168 " --> pdb=" O GLY P 223 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N LEU P 165 " --> pdb=" O SER P 261 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N SER P 261 " --> pdb=" O LEU P 165 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N THR P 171 " --> pdb=" O ILE P 255 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ILE P 255 " --> pdb=" O THR P 171 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ASN P 173 " --> pdb=" O PHE P 253 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N PHE P 253 " --> pdb=" O ASN P 173 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N MET P 258 " --> pdb=" O GLY P 314 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLY P 314 " --> pdb=" O MET P 258 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE P 300 " --> pdb=" O MET P 295 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'f' and resid 111 through 113 removed outlier: 8.243A pdb=" N SER c 25 " --> pdb=" O LEU j 195 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'd' and resid 893 through 894 removed outlier: 7.792A pdb=" N GLU d 893 " --> pdb=" O LEU l 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'd' and resid 934 through 936 Processing sheet with id=AA5, first strand: chain 'e' and resid 461 through 466 removed outlier: 6.411A pdb=" N ILE e 461 " --> pdb=" O LEU f 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'e' and resid 473 through 478 removed outlier: 3.851A pdb=" N THR e 493 " --> pdb=" O PHE e 489 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'e' and resid 506 through 507 removed outlier: 4.284A pdb=" N SER e 506 " --> pdb=" O ASP e 529 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'e' and resid 546 through 550 removed outlier: 6.693A pdb=" N SER e 561 " --> pdb=" O TYR e 547 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA e 549 " --> pdb=" O LEU e 559 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU e 559 " --> pdb=" O ALA e 549 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL e 579 " --> pdb=" O LEU e 569 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'e' and resid 588 through 593 Processing sheet with id=AB1, first strand: chain 'e' and resid 632 through 635 removed outlier: 3.635A pdb=" N ARG e 652 " --> pdb=" O THR e 644 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG e 663 " --> pdb=" O LEU e 653 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASP e 655 " --> pdb=" O CYS e 661 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N CYS e 661 " --> pdb=" O ASP e 655 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'e' and resid 672 through 677 removed outlier: 6.677A pdb=" N GLY e 687 " --> pdb=" O HIS e 673 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU e 675 " --> pdb=" O ALA e 685 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ALA e 685 " --> pdb=" O LEU e 675 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N PHE e 677 " --> pdb=" O PHE e 683 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N PHE e 683 " --> pdb=" O PHE e 677 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ASP e 697 " --> pdb=" O MET e 703 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N MET e 703 " --> pdb=" O ASP e 697 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'e' and resid 716 through 719 removed outlier: 3.779A pdb=" N GLY e 771 " --> pdb=" O LEU e 737 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'e' and resid 782 through 785 removed outlier: 4.239A pdb=" N HIS e 782 " --> pdb=" O ALA e 794 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA e 794 " --> pdb=" O HIS e 782 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'f' and resid 95 through 97 removed outlier: 3.505A pdb=" N LEU f 104 " --> pdb=" O ALA f 97 " (cutoff:3.500A) 550 hydrogen bonds defined for protein. 1617 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: 3.80 Time building geometry restraints manager: 5.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2623 1.33 - 1.45: 3131 1.45 - 1.57: 7708 1.57 - 1.69: 0 1.69 - 1.81: 110 Bond restraints: 13572 Sorted by residual: bond pdb=" C LYS e 445 " pdb=" O LYS e 445 " ideal model delta sigma weight residual 1.237 1.304 -0.067 1.17e-02 7.31e+03 3.28e+01 bond pdb=" N LEU e 285 " pdb=" CA LEU e 285 " ideal model delta sigma weight residual 1.457 1.515 -0.058 1.29e-02 6.01e+03 2.03e+01 bond pdb=" C HIS j 173 " pdb=" O HIS j 173 " ideal model delta sigma weight residual 1.237 1.287 -0.051 1.17e-02 7.31e+03 1.88e+01 bond pdb=" C ASP e 522 " pdb=" O ASP e 522 " ideal model delta sigma weight residual 1.235 1.289 -0.054 1.26e-02 6.30e+03 1.81e+01 bond pdb=" C HIS m 70 " pdb=" O HIS m 70 " ideal model delta sigma weight residual 1.236 1.285 -0.048 1.15e-02 7.56e+03 1.75e+01 ... (remaining 13567 not shown) Histogram of bond angle deviations from ideal: 98.01 - 105.30: 309 105.30 - 112.60: 6743 112.60 - 119.89: 5417 119.89 - 127.19: 5722 127.19 - 134.48: 133 Bond angle restraints: 18324 Sorted by residual: angle pdb=" O PRO f 149 " pdb=" C PRO f 149 " pdb=" N PRO f 150 " ideal model delta sigma weight residual 121.31 125.51 -4.20 4.60e-01 4.73e+00 8.33e+01 angle pdb=" N PRO k 180 " pdb=" CA PRO k 180 " pdb=" C PRO k 180 " ideal model delta sigma weight residual 110.70 119.01 -8.31 1.22e+00 6.72e-01 4.64e+01 angle pdb=" N PRO P 207 " pdb=" CA PRO P 207 " pdb=" C PRO P 207 " ideal model delta sigma weight residual 112.47 100.10 12.37 2.06e+00 2.36e-01 3.61e+01 angle pdb=" N PRO f 150 " pdb=" CA PRO f 150 " pdb=" C PRO f 150 " ideal model delta sigma weight residual 110.70 117.46 -6.76 1.22e+00 6.72e-01 3.07e+01 angle pdb=" C LYS m 71 " pdb=" CA LYS m 71 " pdb=" CB LYS m 71 " ideal model delta sigma weight residual 110.79 119.79 -9.00 1.66e+00 3.63e-01 2.94e+01 ... (remaining 18319 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 7386 17.74 - 35.48: 738 35.48 - 53.22: 145 53.22 - 70.96: 32 70.96 - 88.70: 11 Dihedral angle restraints: 8312 sinusoidal: 3466 harmonic: 4846 Sorted by residual: dihedral pdb=" C LYS m 71 " pdb=" N LYS m 71 " pdb=" CA LYS m 71 " pdb=" CB LYS m 71 " ideal model delta harmonic sigma weight residual -122.60 -137.43 14.83 0 2.50e+00 1.60e-01 3.52e+01 dihedral pdb=" C PHE e 267 " pdb=" N PHE e 267 " pdb=" CA PHE e 267 " pdb=" CB PHE e 267 " ideal model delta harmonic sigma weight residual -122.60 -135.42 12.82 0 2.50e+00 1.60e-01 2.63e+01 dihedral pdb=" N LYS m 71 " pdb=" C LYS m 71 " pdb=" CA LYS m 71 " pdb=" CB LYS m 71 " ideal model delta harmonic sigma weight residual 122.80 134.76 -11.96 0 2.50e+00 1.60e-01 2.29e+01 ... (remaining 8309 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 1670 0.099 - 0.197: 305 0.197 - 0.296: 48 0.296 - 0.395: 4 0.395 - 0.493: 3 Chirality restraints: 2030 Sorted by residual: chirality pdb=" CB ILE f 92 " pdb=" CA ILE f 92 " pdb=" CG1 ILE f 92 " pdb=" CG2 ILE f 92 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.49 2.00e-01 2.50e+01 6.08e+00 chirality pdb=" CA LYS m 71 " pdb=" N LYS m 71 " pdb=" C LYS m 71 " pdb=" CB LYS m 71 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.93e+00 chirality pdb=" CA PHE e 267 " pdb=" N PHE e 267 " pdb=" C PHE e 267 " pdb=" CB PHE e 267 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.04e+00 ... (remaining 2027 not shown) Planarity restraints: 2364 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU e 285 " 0.023 2.00e-02 2.50e+03 4.58e-02 2.10e+01 pdb=" C LEU e 285 " -0.079 2.00e-02 2.50e+03 pdb=" O LEU e 285 " 0.029 2.00e-02 2.50e+03 pdb=" N THR e 286 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS e 449 " 0.020 2.00e-02 2.50e+03 4.02e-02 1.61e+01 pdb=" C LYS e 449 " -0.069 2.00e-02 2.50e+03 pdb=" O LYS e 449 " 0.025 2.00e-02 2.50e+03 pdb=" N ARG e 450 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS e 508 " 0.019 2.00e-02 2.50e+03 3.84e-02 1.48e+01 pdb=" C LYS e 508 " -0.066 2.00e-02 2.50e+03 pdb=" O LYS e 508 " 0.025 2.00e-02 2.50e+03 pdb=" N GLN e 509 " 0.022 2.00e-02 2.50e+03 ... (remaining 2361 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1251 2.75 - 3.29: 12527 3.29 - 3.82: 20864 3.82 - 4.36: 26765 4.36 - 4.90: 44560 Nonbonded interactions: 105967 Sorted by model distance: nonbonded pdb=" OG SER e 562 " pdb=" OD1 ASP e 564 " model vdw 2.209 2.440 nonbonded pdb=" OH TYR d1080 " pdb=" OD2 ASP e 606 " model vdw 2.264 2.440 nonbonded pdb=" OG1 THR e 474 " pdb=" O VAL e 546 " model vdw 2.277 2.440 nonbonded pdb=" O LEU j 123 " pdb=" N ASP j 125 " model vdw 2.302 2.520 nonbonded pdb=" N ASP e 277 " pdb=" OD1 ASP e 277 " model vdw 2.321 2.520 ... (remaining 105962 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: 0.000 Normalize map: mean=0, sd=1: 1.610 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: 0.010 Extract box with map and model: 7.300 Check model and map are aligned: 0.190 Set scattering table: 0.110 Process input model: 33.630 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 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 : 0.008 0.067 13572 Z= 0.496 Angle : 1.065 12.371 18324 Z= 0.735 Chirality : 0.079 0.493 2030 Planarity : 0.008 0.069 2364 Dihedral : 14.832 88.705 5166 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.41 % Favored : 93.34 % Rotamer: Outliers : 2.11 % Allowed : 7.83 % Favored : 90.06 % Cbeta Deviations : 0.32 % 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: -3.03 (0.20), residues: 1622 helix: -1.32 (0.20), residues: 718 sheet: -2.37 (0.33), residues: 200 loop : -2.56 (0.20), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP e 612 HIS 0.007 0.001 HIS e 584 PHE 0.025 0.002 PHE e 600 TYR 0.027 0.002 TYR j 216 ARG 0.009 0.000 ARG e 682 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 1474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 421 time to evaluate : 1.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 36 ASP cc_start: 0.7979 (t0) cc_final: 0.7376 (t0) REVERT: c 89 PRO cc_start: 0.8081 (Cg_exo) cc_final: 0.7559 (Cg_endo) REVERT: e 270 ASP cc_start: 0.7350 (OUTLIER) cc_final: 0.6891 (t0) REVERT: e 282 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7439 (mt) REVERT: f 58 MET cc_start: 0.7737 (ttp) cc_final: 0.7187 (ttt) outliers start: 31 outliers final: 9 residues processed: 438 average time/residue: 0.3725 time to fit residues: 215.9393 Evaluate side-chains 360 residues out of total 1474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 349 time to evaluate : 1.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 24 ASP Chi-restraints excluded: chain e residue 268 HIS Chi-restraints excluded: chain e residue 270 ASP Chi-restraints excluded: chain e residue 277 ASP Chi-restraints excluded: chain e residue 282 LEU Chi-restraints excluded: chain e residue 546 VAL Chi-restraints excluded: chain e residue 579 VAL Chi-restraints excluded: chain m residue 55 ASP Chi-restraints excluded: chain m residue 58 GLU Chi-restraints excluded: chain m residue 77 ARG Chi-restraints excluded: chain m residue 84 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 124 optimal weight: 0.3980 chunk 48 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 144 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 189 ASN P 193 ASN P 327 ASN ** c 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 19 GLN c 85 HIS d 912 ASN d1069 ASN ** e 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 256 HIS ** e 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 425 ASN e 673 HIS j 160 GLN j 173 HIS k 139 GLN l 101 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13572 Z= 0.237 Angle : 0.672 12.017 18324 Z= 0.341 Chirality : 0.044 0.226 2030 Planarity : 0.006 0.052 2364 Dihedral : 5.875 44.111 1830 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.65 % Allowed : 16.27 % Favored : 81.08 % 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: -1.95 (0.20), residues: 1622 helix: -0.30 (0.19), residues: 715 sheet: -1.88 (0.36), residues: 187 loop : -2.14 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP e 612 HIS 0.006 0.001 HIS l 119 PHE 0.016 0.002 PHE e 264 TYR 0.020 0.002 TYR j 216 ARG 0.007 0.001 ARG f 124 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 365 time to evaluate : 1.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 105 ASN cc_start: 0.7832 (m-40) cc_final: 0.7289 (m110) REVERT: f 58 MET cc_start: 0.7890 (ttp) cc_final: 0.7546 (ttt) REVERT: j 122 GLN cc_start: 0.8081 (OUTLIER) cc_final: 0.7486 (tt0) REVERT: j 161 LYS cc_start: 0.8122 (tmtt) cc_final: 0.7912 (tttm) REVERT: k 195 LYS cc_start: 0.7961 (tttm) cc_final: 0.7687 (tttt) REVERT: m 58 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.7103 (tm-30) outliers start: 39 outliers final: 21 residues processed: 382 average time/residue: 0.3584 time to fit residues: 180.4037 Evaluate side-chains 363 residues out of total 1474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 340 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 219 MET Chi-restraints excluded: chain P residue 236 LYS Chi-restraints excluded: chain P residue 280 PHE Chi-restraints excluded: chain e residue 268 HIS Chi-restraints excluded: chain e residue 277 ASP Chi-restraints excluded: chain e residue 546 VAL Chi-restraints excluded: chain e residue 632 CYS Chi-restraints excluded: chain e residue 700 HIS Chi-restraints excluded: chain e residue 712 ASP Chi-restraints excluded: chain e residue 778 THR Chi-restraints excluded: chain e residue 786 THR Chi-restraints excluded: chain i residue 12 MET Chi-restraints excluded: chain i residue 56 ILE Chi-restraints excluded: chain i residue 59 SER Chi-restraints excluded: chain j residue 122 GLN Chi-restraints excluded: chain k residue 140 SER Chi-restraints excluded: chain k residue 145 SER Chi-restraints excluded: chain k residue 155 SER Chi-restraints excluded: chain k residue 173 CYS Chi-restraints excluded: chain l residue 101 GLN Chi-restraints excluded: chain l residue 144 THR Chi-restraints excluded: chain m residue 58 GLU Chi-restraints excluded: chain m residue 81 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 80 optimal weight: 1.9990 chunk 44 optimal weight: 0.0040 chunk 120 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 144 optimal weight: 0.9990 chunk 156 optimal weight: 0.6980 chunk 128 optimal weight: 2.9990 chunk 143 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 116 optimal weight: 0.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 256 GLN P 327 ASN c 16 GLN c 78 HIS ** e 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 328 GLN k 139 GLN k 186 HIS l 56 GLN l 148 HIS ** m 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13572 Z= 0.223 Angle : 0.635 12.021 18324 Z= 0.316 Chirality : 0.043 0.237 2030 Planarity : 0.005 0.052 2364 Dihedral : 5.140 41.818 1814 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.06 % Allowed : 17.63 % Favored : 79.31 % 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: -1.14 (0.21), residues: 1622 helix: 0.49 (0.20), residues: 719 sheet: -1.43 (0.37), residues: 190 loop : -1.88 (0.22), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP e 612 HIS 0.006 0.001 HIS e 256 PHE 0.015 0.001 PHE m 97 TYR 0.022 0.002 TYR e 275 ARG 0.008 0.001 ARG f 124 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 351 time to evaluate : 1.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 258 MET cc_start: 0.3352 (ptp) cc_final: 0.2495 (ptp) REVERT: e 638 ASN cc_start: 0.7642 (m110) cc_final: 0.7379 (m110) REVERT: e 787 ARG cc_start: 0.6661 (mmm160) cc_final: 0.6415 (mmm-85) REVERT: f 58 MET cc_start: 0.7853 (ttp) cc_final: 0.7499 (ttt) REVERT: i 76 GLN cc_start: 0.7273 (tt0) cc_final: 0.7032 (tt0) REVERT: j 161 LYS cc_start: 0.8161 (tmtt) cc_final: 0.7951 (tttm) REVERT: l 60 LYS cc_start: 0.7594 (tttt) cc_final: 0.6384 (ttmm) outliers start: 45 outliers final: 29 residues processed: 368 average time/residue: 0.3463 time to fit residues: 168.3394 Evaluate side-chains 363 residues out of total 1474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 334 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 209 THR Chi-restraints excluded: chain P residue 254 LYS Chi-restraints excluded: chain P residue 280 PHE Chi-restraints excluded: chain P residue 292 ILE Chi-restraints excluded: chain P residue 332 LEU Chi-restraints excluded: chain d residue 915 GLU Chi-restraints excluded: chain d residue 1059 ASN Chi-restraints excluded: chain d residue 1081 LYS Chi-restraints excluded: chain e residue 268 HIS Chi-restraints excluded: chain e residue 277 ASP Chi-restraints excluded: chain e residue 278 ASP Chi-restraints excluded: chain e residue 298 LEU Chi-restraints excluded: chain e residue 476 VAL Chi-restraints excluded: chain e residue 546 VAL Chi-restraints excluded: chain e residue 612 TRP Chi-restraints excluded: chain e residue 632 CYS Chi-restraints excluded: chain e residue 700 HIS Chi-restraints excluded: chain e residue 712 ASP Chi-restraints excluded: chain e residue 778 THR Chi-restraints excluded: chain e residue 786 THR Chi-restraints excluded: chain f residue 26 MET Chi-restraints excluded: chain i residue 12 MET Chi-restraints excluded: chain i residue 56 ILE Chi-restraints excluded: chain i residue 59 SER Chi-restraints excluded: chain k residue 140 SER Chi-restraints excluded: chain k residue 173 CYS Chi-restraints excluded: chain l residue 144 THR Chi-restraints excluded: chain m residue 48 ASN Chi-restraints excluded: chain m residue 81 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 142 optimal weight: 0.9990 chunk 108 optimal weight: 9.9990 chunk 75 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 97 optimal weight: 0.0010 chunk 145 optimal weight: 0.9980 chunk 153 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 chunk 127 optimal weight: 0.7980 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 105 ASN e 290 HIS ** e 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 784 HIS ** i 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 122 GLN ** m 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13572 Z= 0.237 Angle : 0.641 13.883 18324 Z= 0.316 Chirality : 0.043 0.182 2030 Planarity : 0.005 0.051 2364 Dihedral : 4.872 40.229 1811 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.54 % Allowed : 19.67 % Favored : 76.79 % 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: -0.74 (0.21), residues: 1622 helix: 0.85 (0.20), residues: 718 sheet: -1.14 (0.37), residues: 195 loop : -1.72 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP e 612 HIS 0.006 0.001 HIS e 290 PHE 0.012 0.001 PHE m 97 TYR 0.025 0.002 TYR e 275 ARG 0.016 0.001 ARG P 318 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 340 time to evaluate : 1.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 213 MET cc_start: 0.5806 (mmm) cc_final: 0.4957 (mmp) REVERT: e 638 ASN cc_start: 0.7622 (m110) cc_final: 0.7386 (m-40) REVERT: e 663 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.6944 (mtt90) REVERT: e 787 ARG cc_start: 0.6774 (mmm160) cc_final: 0.6504 (mmm-85) REVERT: f 58 MET cc_start: 0.7908 (ttp) cc_final: 0.7554 (ttt) REVERT: j 161 LYS cc_start: 0.8122 (tmtt) cc_final: 0.7878 (tttm) outliers start: 52 outliers final: 38 residues processed: 362 average time/residue: 0.3449 time to fit residues: 165.6064 Evaluate side-chains 366 residues out of total 1474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 327 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 225 LYS Chi-restraints excluded: chain P residue 236 LYS Chi-restraints excluded: chain P residue 254 LYS Chi-restraints excluded: chain P residue 280 PHE Chi-restraints excluded: chain P residue 286 GLU Chi-restraints excluded: chain P residue 292 ILE Chi-restraints excluded: chain P residue 332 LEU Chi-restraints excluded: chain c residue 26 VAL Chi-restraints excluded: chain c residue 64 ASP Chi-restraints excluded: chain c residue 107 LEU Chi-restraints excluded: chain d residue 885 ILE Chi-restraints excluded: chain d residue 915 GLU Chi-restraints excluded: chain d residue 1059 ASN Chi-restraints excluded: chain d residue 1078 LEU Chi-restraints excluded: chain d residue 1081 LYS Chi-restraints excluded: chain e residue 277 ASP Chi-restraints excluded: chain e residue 278 ASP Chi-restraints excluded: chain e residue 298 LEU Chi-restraints excluded: chain e residue 434 ASP Chi-restraints excluded: chain e residue 476 VAL Chi-restraints excluded: chain e residue 546 VAL Chi-restraints excluded: chain e residue 574 THR Chi-restraints excluded: chain e residue 612 TRP Chi-restraints excluded: chain e residue 632 CYS Chi-restraints excluded: chain e residue 663 ARG Chi-restraints excluded: chain e residue 692 ARG Chi-restraints excluded: chain e residue 700 HIS Chi-restraints excluded: chain e residue 712 ASP Chi-restraints excluded: chain e residue 778 THR Chi-restraints excluded: chain e residue 786 THR Chi-restraints excluded: chain f residue 26 MET Chi-restraints excluded: chain i residue 12 MET Chi-restraints excluded: chain i residue 56 ILE Chi-restraints excluded: chain i residue 59 SER Chi-restraints excluded: chain k residue 173 CYS Chi-restraints excluded: chain l residue 101 GLN Chi-restraints excluded: chain l residue 144 THR Chi-restraints excluded: chain m residue 48 ASN Chi-restraints excluded: chain m residue 81 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 87 optimal weight: 0.8980 chunk 2 optimal weight: 40.0000 chunk 114 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 131 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 78 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 104 ASN c 105 ASN ** e 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 784 HIS ** i 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 122 GLN ** m 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 13572 Z= 0.307 Angle : 0.659 13.386 18324 Z= 0.326 Chirality : 0.044 0.188 2030 Planarity : 0.005 0.046 2364 Dihedral : 4.809 34.253 1809 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.88 % Allowed : 20.90 % Favored : 75.22 % 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: -0.62 (0.21), residues: 1622 helix: 0.99 (0.20), residues: 722 sheet: -1.18 (0.37), residues: 197 loop : -1.69 (0.23), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP e 612 HIS 0.005 0.001 HIS e 584 PHE 0.019 0.002 PHE e 264 TYR 0.026 0.002 TYR e 275 ARG 0.009 0.001 ARG P 231 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 341 time to evaluate : 1.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 787 ARG cc_start: 0.6787 (mmm160) cc_final: 0.6498 (mmm-85) REVERT: f 58 MET cc_start: 0.7891 (ttp) cc_final: 0.7591 (ttt) REVERT: j 161 LYS cc_start: 0.8171 (tmtt) cc_final: 0.7907 (tttm) outliers start: 57 outliers final: 46 residues processed: 364 average time/residue: 0.3430 time to fit residues: 166.5544 Evaluate side-chains 375 residues out of total 1474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 329 time to evaluate : 1.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 209 THR Chi-restraints excluded: chain P residue 225 LYS Chi-restraints excluded: chain P residue 236 LYS Chi-restraints excluded: chain P residue 280 PHE Chi-restraints excluded: chain P residue 286 GLU Chi-restraints excluded: chain P residue 292 ILE Chi-restraints excluded: chain c residue 26 VAL Chi-restraints excluded: chain c residue 64 ASP Chi-restraints excluded: chain c residue 77 LEU Chi-restraints excluded: chain c residue 107 LEU Chi-restraints excluded: chain d residue 885 ILE Chi-restraints excluded: chain d residue 915 GLU Chi-restraints excluded: chain d residue 1059 ASN Chi-restraints excluded: chain d residue 1078 LEU Chi-restraints excluded: chain d residue 1081 LYS Chi-restraints excluded: chain e residue 205 TYR Chi-restraints excluded: chain e residue 268 HIS Chi-restraints excluded: chain e residue 277 ASP Chi-restraints excluded: chain e residue 278 ASP Chi-restraints excluded: chain e residue 298 LEU Chi-restraints excluded: chain e residue 328 GLN Chi-restraints excluded: chain e residue 434 ASP Chi-restraints excluded: chain e residue 476 VAL Chi-restraints excluded: chain e residue 546 VAL Chi-restraints excluded: chain e residue 554 ASP Chi-restraints excluded: chain e residue 563 GLU Chi-restraints excluded: chain e residue 574 THR Chi-restraints excluded: chain e residue 612 TRP Chi-restraints excluded: chain e residue 632 CYS Chi-restraints excluded: chain e residue 674 SER Chi-restraints excluded: chain e residue 700 HIS Chi-restraints excluded: chain e residue 712 ASP Chi-restraints excluded: chain e residue 778 THR Chi-restraints excluded: chain e residue 786 THR Chi-restraints excluded: chain f residue 26 MET Chi-restraints excluded: chain i residue 12 MET Chi-restraints excluded: chain i residue 56 ILE Chi-restraints excluded: chain i residue 59 SER Chi-restraints excluded: chain i residue 102 THR Chi-restraints excluded: chain j residue 121 MET Chi-restraints excluded: chain j residue 215 HIS Chi-restraints excluded: chain k residue 155 SER Chi-restraints excluded: chain k residue 173 CYS Chi-restraints excluded: chain l residue 101 GLN Chi-restraints excluded: chain l residue 144 THR Chi-restraints excluded: chain m residue 81 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 138 optimal weight: 0.5980 chunk 30 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 50 optimal weight: 0.4980 chunk 80 optimal weight: 0.9980 chunk 148 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 27 GLN c 85 HIS c 105 ASN ** e 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 271 GLN e 425 ASN ** e 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 784 HIS ** i 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.4042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13572 Z= 0.249 Angle : 0.645 14.621 18324 Z= 0.319 Chirality : 0.044 0.285 2030 Planarity : 0.005 0.049 2364 Dihedral : 4.717 32.860 1809 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 4.42 % Allowed : 20.63 % Favored : 74.95 % 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: -0.46 (0.21), residues: 1622 helix: 1.16 (0.20), residues: 721 sheet: -1.06 (0.37), residues: 195 loop : -1.66 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP e 612 HIS 0.004 0.001 HIS e 584 PHE 0.042 0.002 PHE P 335 TYR 0.029 0.002 TYR e 275 ARG 0.009 0.001 ARG f 124 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 329 time to evaluate : 1.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 950 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7816 (tt) REVERT: e 663 ARG cc_start: 0.8927 (OUTLIER) cc_final: 0.7202 (mtt90) REVERT: e 787 ARG cc_start: 0.6811 (mmm160) cc_final: 0.6535 (mmm-85) REVERT: f 9 LEU cc_start: 0.3680 (OUTLIER) cc_final: 0.3478 (tt) REVERT: f 58 MET cc_start: 0.7926 (ttp) cc_final: 0.7614 (ttt) REVERT: i 34 ARG cc_start: 0.7479 (OUTLIER) cc_final: 0.6497 (mtp180) REVERT: i 78 ARG cc_start: 0.6808 (OUTLIER) cc_final: 0.6283 (mmt90) REVERT: j 165 ASP cc_start: 0.6803 (m-30) cc_final: 0.6254 (m-30) outliers start: 65 outliers final: 47 residues processed: 361 average time/residue: 0.3525 time to fit residues: 168.4129 Evaluate side-chains 370 residues out of total 1474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 318 time to evaluate : 1.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 209 THR Chi-restraints excluded: chain P residue 225 LYS Chi-restraints excluded: chain P residue 236 LYS Chi-restraints excluded: chain P residue 286 GLU Chi-restraints excluded: chain P residue 292 ILE Chi-restraints excluded: chain P residue 332 LEU Chi-restraints excluded: chain c residue 12 VAL Chi-restraints excluded: chain c residue 26 VAL Chi-restraints excluded: chain c residue 64 ASP Chi-restraints excluded: chain c residue 77 LEU Chi-restraints excluded: chain c residue 107 LEU Chi-restraints excluded: chain d residue 885 ILE Chi-restraints excluded: chain d residue 915 GLU Chi-restraints excluded: chain d residue 950 LEU Chi-restraints excluded: chain d residue 1059 ASN Chi-restraints excluded: chain d residue 1078 LEU Chi-restraints excluded: chain d residue 1081 LYS Chi-restraints excluded: chain e residue 205 TYR Chi-restraints excluded: chain e residue 268 HIS Chi-restraints excluded: chain e residue 277 ASP Chi-restraints excluded: chain e residue 298 LEU Chi-restraints excluded: chain e residue 434 ASP Chi-restraints excluded: chain e residue 448 THR Chi-restraints excluded: chain e residue 476 VAL Chi-restraints excluded: chain e residue 546 VAL Chi-restraints excluded: chain e residue 554 ASP Chi-restraints excluded: chain e residue 574 THR Chi-restraints excluded: chain e residue 612 TRP Chi-restraints excluded: chain e residue 632 CYS Chi-restraints excluded: chain e residue 663 ARG Chi-restraints excluded: chain e residue 674 SER Chi-restraints excluded: chain e residue 692 ARG Chi-restraints excluded: chain e residue 700 HIS Chi-restraints excluded: chain e residue 712 ASP Chi-restraints excluded: chain e residue 778 THR Chi-restraints excluded: chain e residue 786 THR Chi-restraints excluded: chain f residue 9 LEU Chi-restraints excluded: chain f residue 18 SER Chi-restraints excluded: chain f residue 26 MET Chi-restraints excluded: chain f residue 80 VAL Chi-restraints excluded: chain i residue 12 MET Chi-restraints excluded: chain i residue 34 ARG Chi-restraints excluded: chain i residue 56 ILE Chi-restraints excluded: chain i residue 59 SER Chi-restraints excluded: chain i residue 78 ARG Chi-restraints excluded: chain i residue 102 THR Chi-restraints excluded: chain i residue 129 LEU Chi-restraints excluded: chain j residue 215 HIS Chi-restraints excluded: chain k residue 173 CYS Chi-restraints excluded: chain l residue 101 GLN Chi-restraints excluded: chain l residue 144 THR Chi-restraints excluded: chain m residue 81 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 17 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 129 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 153 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 93 optimal weight: 0.0570 chunk 70 optimal weight: 0.0670 chunk 94 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 overall best weight: 0.4836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 16 GLN c 85 HIS d 936 GLN ** e 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.4274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13572 Z= 0.204 Angle : 0.641 13.950 18324 Z= 0.318 Chirality : 0.043 0.227 2030 Planarity : 0.004 0.044 2364 Dihedral : 4.551 31.485 1809 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 3.81 % Allowed : 21.65 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.21), residues: 1622 helix: 1.28 (0.20), residues: 720 sheet: -1.00 (0.37), residues: 195 loop : -1.59 (0.23), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP e 612 HIS 0.003 0.001 HIS l 119 PHE 0.046 0.001 PHE e 267 TYR 0.022 0.001 TYR P 322 ARG 0.011 0.001 ARG P 231 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 332 time to evaluate : 1.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 65 ASP cc_start: 0.6916 (m-30) cc_final: 0.6716 (m-30) REVERT: d 950 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7807 (tt) REVERT: e 213 MET cc_start: 0.5486 (mmm) cc_final: 0.4780 (mmm) REVERT: e 663 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.7140 (mtt90) REVERT: e 787 ARG cc_start: 0.6928 (mmm160) cc_final: 0.6710 (mmm-85) REVERT: f 58 MET cc_start: 0.7903 (ttp) cc_final: 0.7572 (ttt) REVERT: m 104 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.7054 (mm) outliers start: 56 outliers final: 44 residues processed: 361 average time/residue: 0.3436 time to fit residues: 165.2933 Evaluate side-chains 363 residues out of total 1474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 316 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 172 VAL Chi-restraints excluded: chain P residue 209 THR Chi-restraints excluded: chain P residue 225 LYS Chi-restraints excluded: chain P residue 236 LYS Chi-restraints excluded: chain P residue 286 GLU Chi-restraints excluded: chain c residue 26 VAL Chi-restraints excluded: chain c residue 64 ASP Chi-restraints excluded: chain c residue 96 ILE Chi-restraints excluded: chain c residue 107 LEU Chi-restraints excluded: chain d residue 885 ILE Chi-restraints excluded: chain d residue 915 GLU Chi-restraints excluded: chain d residue 950 LEU Chi-restraints excluded: chain d residue 1059 ASN Chi-restraints excluded: chain d residue 1078 LEU Chi-restraints excluded: chain d residue 1081 LYS Chi-restraints excluded: chain e residue 205 TYR Chi-restraints excluded: chain e residue 277 ASP Chi-restraints excluded: chain e residue 298 LEU Chi-restraints excluded: chain e residue 476 VAL Chi-restraints excluded: chain e residue 546 VAL Chi-restraints excluded: chain e residue 554 ASP Chi-restraints excluded: chain e residue 563 GLU Chi-restraints excluded: chain e residue 574 THR Chi-restraints excluded: chain e residue 612 TRP Chi-restraints excluded: chain e residue 632 CYS Chi-restraints excluded: chain e residue 663 ARG Chi-restraints excluded: chain e residue 692 ARG Chi-restraints excluded: chain e residue 700 HIS Chi-restraints excluded: chain e residue 712 ASP Chi-restraints excluded: chain e residue 778 THR Chi-restraints excluded: chain e residue 786 THR Chi-restraints excluded: chain f residue 18 SER Chi-restraints excluded: chain f residue 52 GLN Chi-restraints excluded: chain i residue 12 MET Chi-restraints excluded: chain i residue 59 SER Chi-restraints excluded: chain i residue 78 ARG Chi-restraints excluded: chain i residue 102 THR Chi-restraints excluded: chain i residue 129 LEU Chi-restraints excluded: chain j residue 123 LEU Chi-restraints excluded: chain j residue 215 HIS Chi-restraints excluded: chain k residue 123 MET Chi-restraints excluded: chain k residue 173 CYS Chi-restraints excluded: chain k residue 195 LYS Chi-restraints excluded: chain l residue 101 GLN Chi-restraints excluded: chain l residue 144 THR Chi-restraints excluded: chain m residue 81 VAL Chi-restraints excluded: chain m residue 104 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 91 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 97 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 139 optimal weight: 0.6980 chunk 146 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 85 HIS ** e 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 784 HIS ** i 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 199 GLN ** m 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.4406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13572 Z= 0.265 Angle : 0.698 14.982 18324 Z= 0.341 Chirality : 0.044 0.314 2030 Planarity : 0.005 0.048 2364 Dihedral : 4.574 31.803 1809 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.74 % Allowed : 23.01 % Favored : 73.25 % 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: -0.32 (0.21), residues: 1622 helix: 1.25 (0.20), residues: 720 sheet: -1.10 (0.37), residues: 197 loop : -1.51 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP e 330 HIS 0.004 0.001 HIS e 584 PHE 0.034 0.002 PHE P 335 TYR 0.041 0.002 TYR P 322 ARG 0.010 0.001 ARG f 124 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 329 time to evaluate : 1.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 950 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7811 (tt) REVERT: e 663 ARG cc_start: 0.8964 (OUTLIER) cc_final: 0.7271 (mtt90) REVERT: e 787 ARG cc_start: 0.6968 (mmm160) cc_final: 0.6720 (mmm-85) REVERT: f 58 MET cc_start: 0.7915 (ttp) cc_final: 0.7582 (ttt) REVERT: i 34 ARG cc_start: 0.7529 (OUTLIER) cc_final: 0.6506 (mtp180) REVERT: m 104 LEU cc_start: 0.7428 (OUTLIER) cc_final: 0.7071 (mm) outliers start: 55 outliers final: 42 residues processed: 358 average time/residue: 0.3564 time to fit residues: 168.4972 Evaluate side-chains 359 residues out of total 1474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 313 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 209 THR Chi-restraints excluded: chain P residue 236 LYS Chi-restraints excluded: chain P residue 286 GLU Chi-restraints excluded: chain P residue 292 ILE Chi-restraints excluded: chain c residue 26 VAL Chi-restraints excluded: chain c residue 64 ASP Chi-restraints excluded: chain c residue 77 LEU Chi-restraints excluded: chain c residue 107 LEU Chi-restraints excluded: chain d residue 885 ILE Chi-restraints excluded: chain d residue 915 GLU Chi-restraints excluded: chain d residue 950 LEU Chi-restraints excluded: chain d residue 1059 ASN Chi-restraints excluded: chain d residue 1078 LEU Chi-restraints excluded: chain d residue 1081 LYS Chi-restraints excluded: chain e residue 205 TYR Chi-restraints excluded: chain e residue 277 ASP Chi-restraints excluded: chain e residue 298 LEU Chi-restraints excluded: chain e residue 448 THR Chi-restraints excluded: chain e residue 476 VAL Chi-restraints excluded: chain e residue 546 VAL Chi-restraints excluded: chain e residue 563 GLU Chi-restraints excluded: chain e residue 574 THR Chi-restraints excluded: chain e residue 612 TRP Chi-restraints excluded: chain e residue 632 CYS Chi-restraints excluded: chain e residue 663 ARG Chi-restraints excluded: chain e residue 700 HIS Chi-restraints excluded: chain e residue 704 VAL Chi-restraints excluded: chain e residue 712 ASP Chi-restraints excluded: chain e residue 778 THR Chi-restraints excluded: chain e residue 786 THR Chi-restraints excluded: chain f residue 18 SER Chi-restraints excluded: chain f residue 52 GLN Chi-restraints excluded: chain i residue 12 MET Chi-restraints excluded: chain i residue 34 ARG Chi-restraints excluded: chain i residue 59 SER Chi-restraints excluded: chain i residue 78 ARG Chi-restraints excluded: chain i residue 102 THR Chi-restraints excluded: chain i residue 129 LEU Chi-restraints excluded: chain j residue 123 LEU Chi-restraints excluded: chain j residue 215 HIS Chi-restraints excluded: chain k residue 123 MET Chi-restraints excluded: chain k residue 173 CYS Chi-restraints excluded: chain l residue 101 GLN Chi-restraints excluded: chain l residue 144 THR Chi-restraints excluded: chain m residue 81 VAL Chi-restraints excluded: chain m residue 104 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 133 optimal weight: 0.6980 chunk 142 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 chunk 151 optimal weight: 0.6980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 167 ASN P 327 ASN c 71 GLN c 85 HIS ** e 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 784 HIS i 126 ASN l 73 ASN ** m 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.4505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 13572 Z= 0.442 Angle : 0.767 15.177 18324 Z= 0.378 Chirality : 0.048 0.332 2030 Planarity : 0.005 0.046 2364 Dihedral : 4.863 33.902 1809 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 3.34 % Allowed : 23.49 % Favored : 73.18 % 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: -0.52 (0.21), residues: 1622 helix: 1.03 (0.20), residues: 723 sheet: -1.38 (0.35), residues: 204 loop : -1.50 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP e 330 HIS 0.006 0.001 HIS e 256 PHE 0.031 0.002 PHE e 267 TYR 0.020 0.002 TYR P 322 ARG 0.009 0.001 ARG f 124 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 318 time to evaluate : 1.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 19 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.7104 (tp40) REVERT: c 73 MET cc_start: 0.7902 (mmm) cc_final: 0.7628 (mtp) REVERT: d 950 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7849 (tt) REVERT: f 58 MET cc_start: 0.7927 (ttp) cc_final: 0.7624 (ttt) REVERT: i 34 ARG cc_start: 0.7556 (OUTLIER) cc_final: 0.6586 (mtp180) REVERT: i 78 ARG cc_start: 0.6763 (OUTLIER) cc_final: 0.6280 (mmt90) REVERT: m 104 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.7044 (mm) outliers start: 49 outliers final: 39 residues processed: 343 average time/residue: 0.3542 time to fit residues: 161.1244 Evaluate side-chains 356 residues out of total 1474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 312 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 209 THR Chi-restraints excluded: chain P residue 236 LYS Chi-restraints excluded: chain P residue 286 GLU Chi-restraints excluded: chain P residue 292 ILE Chi-restraints excluded: chain c residue 12 VAL Chi-restraints excluded: chain c residue 19 GLN Chi-restraints excluded: chain c residue 64 ASP Chi-restraints excluded: chain c residue 77 LEU Chi-restraints excluded: chain c residue 107 LEU Chi-restraints excluded: chain d residue 871 THR Chi-restraints excluded: chain d residue 885 ILE Chi-restraints excluded: chain d residue 915 GLU Chi-restraints excluded: chain d residue 950 LEU Chi-restraints excluded: chain d residue 1059 ASN Chi-restraints excluded: chain d residue 1078 LEU Chi-restraints excluded: chain d residue 1081 LYS Chi-restraints excluded: chain e residue 205 TYR Chi-restraints excluded: chain e residue 277 ASP Chi-restraints excluded: chain e residue 298 LEU Chi-restraints excluded: chain e residue 476 VAL Chi-restraints excluded: chain e residue 546 VAL Chi-restraints excluded: chain e residue 563 GLU Chi-restraints excluded: chain e residue 574 THR Chi-restraints excluded: chain e residue 612 TRP Chi-restraints excluded: chain e residue 632 CYS Chi-restraints excluded: chain e residue 700 HIS Chi-restraints excluded: chain e residue 778 THR Chi-restraints excluded: chain e residue 786 THR Chi-restraints excluded: chain f residue 18 SER Chi-restraints excluded: chain f residue 26 MET Chi-restraints excluded: chain i residue 12 MET Chi-restraints excluded: chain i residue 34 ARG Chi-restraints excluded: chain i residue 59 SER Chi-restraints excluded: chain i residue 78 ARG Chi-restraints excluded: chain i residue 102 THR Chi-restraints excluded: chain i residue 129 LEU Chi-restraints excluded: chain j residue 123 LEU Chi-restraints excluded: chain j residue 215 HIS Chi-restraints excluded: chain l residue 101 GLN Chi-restraints excluded: chain l residue 144 THR Chi-restraints excluded: chain l residue 157 LYS Chi-restraints excluded: chain m residue 31 LEU Chi-restraints excluded: chain m residue 81 VAL Chi-restraints excluded: chain m residue 104 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 92 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 104 optimal weight: 0.6980 chunk 158 optimal weight: 0.9980 chunk 145 optimal weight: 0.8980 chunk 126 optimal weight: 0.6980 chunk 13 optimal weight: 5.9990 chunk 97 optimal weight: 0.0070 chunk 77 optimal weight: 0.1980 chunk 100 optimal weight: 0.7980 chunk 134 optimal weight: 2.9990 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 71 GLN c 85 HIS c 105 ASN ** e 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.4639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13572 Z= 0.215 Angle : 0.716 15.446 18324 Z= 0.351 Chirality : 0.044 0.343 2030 Planarity : 0.004 0.045 2364 Dihedral : 4.645 31.943 1809 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.20 % Allowed : 23.89 % Favored : 72.91 % 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: -0.28 (0.21), residues: 1622 helix: 1.26 (0.20), residues: 721 sheet: -1.06 (0.36), residues: 198 loop : -1.46 (0.24), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP e 330 HIS 0.004 0.001 HIS e 256 PHE 0.028 0.001 PHE P 335 TYR 0.022 0.001 TYR i 120 ARG 0.010 0.001 ARG f 124 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 306 time to evaluate : 1.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 19 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7019 (tp40) REVERT: d 950 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7739 (tt) REVERT: f 58 MET cc_start: 0.7846 (ttp) cc_final: 0.7546 (ttt) REVERT: i 34 ARG cc_start: 0.7504 (OUTLIER) cc_final: 0.6542 (mtp180) outliers start: 47 outliers final: 38 residues processed: 328 average time/residue: 0.3652 time to fit residues: 160.5954 Evaluate side-chains 342 residues out of total 1474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 301 time to evaluate : 1.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 209 THR Chi-restraints excluded: chain P residue 236 LYS Chi-restraints excluded: chain P residue 286 GLU Chi-restraints excluded: chain P residue 292 ILE Chi-restraints excluded: chain c residue 19 GLN Chi-restraints excluded: chain c residue 64 ASP Chi-restraints excluded: chain c residue 77 LEU Chi-restraints excluded: chain c residue 107 LEU Chi-restraints excluded: chain d residue 871 THR Chi-restraints excluded: chain d residue 885 ILE Chi-restraints excluded: chain d residue 915 GLU Chi-restraints excluded: chain d residue 950 LEU Chi-restraints excluded: chain d residue 1055 ILE Chi-restraints excluded: chain d residue 1059 ASN Chi-restraints excluded: chain d residue 1078 LEU Chi-restraints excluded: chain d residue 1081 LYS Chi-restraints excluded: chain e residue 277 ASP Chi-restraints excluded: chain e residue 298 LEU Chi-restraints excluded: chain e residue 476 VAL Chi-restraints excluded: chain e residue 546 VAL Chi-restraints excluded: chain e residue 563 GLU Chi-restraints excluded: chain e residue 574 THR Chi-restraints excluded: chain e residue 612 TRP Chi-restraints excluded: chain e residue 632 CYS Chi-restraints excluded: chain e residue 700 HIS Chi-restraints excluded: chain e residue 704 VAL Chi-restraints excluded: chain e residue 778 THR Chi-restraints excluded: chain e residue 786 THR Chi-restraints excluded: chain f residue 18 SER Chi-restraints excluded: chain i residue 12 MET Chi-restraints excluded: chain i residue 34 ARG Chi-restraints excluded: chain i residue 59 SER Chi-restraints excluded: chain i residue 78 ARG Chi-restraints excluded: chain i residue 102 THR Chi-restraints excluded: chain i residue 129 LEU Chi-restraints excluded: chain j residue 123 LEU Chi-restraints excluded: chain j residue 215 HIS Chi-restraints excluded: chain l residue 101 GLN Chi-restraints excluded: chain m residue 31 LEU Chi-restraints excluded: chain m residue 81 VAL Chi-restraints excluded: chain m residue 102 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 38 optimal weight: 2.9990 chunk 116 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 15 optimal weight: 8.9990 chunk 23 optimal weight: 0.4980 chunk 110 optimal weight: 0.2980 chunk 7 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 166 GLN ** c 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 71 GLN ** e 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 425 ASN ** e 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 784 HIS i 76 GLN ** k 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 150 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.153204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.098176 restraints weight = 18297.197| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.85 r_work: 0.3084 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.4705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 13572 Z= 0.278 Angle : 0.731 15.473 18324 Z= 0.358 Chirality : 0.045 0.328 2030 Planarity : 0.005 0.055 2364 Dihedral : 4.633 32.043 1809 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 3.40 % Allowed : 23.96 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.29 (0.21), residues: 1622 helix: 1.22 (0.20), residues: 722 sheet: -1.09 (0.36), residues: 197 loop : -1.43 (0.23), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP e 330 HIS 0.005 0.001 HIS e 256 PHE 0.031 0.002 PHE m 88 TYR 0.022 0.001 TYR i 120 ARG 0.014 0.001 ARG P 231 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3908.20 seconds wall clock time: 71 minutes 7.53 seconds (4267.53 seconds total)