Starting phenix.real_space_refine on Wed Feb 14 19:10:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpr_16164/02_2024/8bpr_16164_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpr_16164/02_2024/8bpr_16164.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpr_16164/02_2024/8bpr_16164.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpr_16164/02_2024/8bpr_16164.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpr_16164/02_2024/8bpr_16164_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpr_16164/02_2024/8bpr_16164_updated.pdb" } resolution = 3.65 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= 0.028 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: 7 Type Number sf(0) Gaussians Zn 3 6.06 5 P 48 5.49 5 Mg 2 5.21 5 S 19 5.16 5 C 6066 2.51 5 N 1944 2.21 5 O 1973 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 246": "OD1" <-> "OD2" Residue "A ASP 300": "OD1" <-> "OD2" Residue "B TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 151": "OE1" <-> "OE2" Residue "B ASP 293": "OD1" <-> "OD2" Residue "B GLU 294": "OE1" <-> "OE2" Residue "F TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10055 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2660 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 341, 2652 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 322} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 341, 2652 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 322} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 2692 Chain: "B" Number of atoms: 2643 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 340, 2635 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 17, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Conformer: "B" Number of residues, atoms: 340, 2635 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 17, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 bond proxies already assigned to first conformer: 2673 Chain: "C" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 203 Classifications: {'peptide': 41} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 3, 'PHE:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 59 Chain: "D" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 774 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 118} Link IDs: {'PTRANS': 6, 'TRANS': 150} Chain breaks: 4 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 436 Unresolved non-hydrogen angles: 558 Unresolved non-hydrogen dihedrals: 346 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 4, 'TYR:plan': 5, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 21, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 245 Chain: "E" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 861 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 132} Link IDs: {'PTRANS': 8, 'TRANS': 166} Chain breaks: 3 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 488 Unresolved non-hydrogen angles: 622 Unresolved non-hydrogen dihedrals: 389 Unresolved non-hydrogen chiralities: 53 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 3, 'HIS:plan': 3, 'PHE:plan': 3, 'GLU:plan': 24, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 262 Chain: "F" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1005 Classifications: {'peptide': 154} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 6, 'TRANS': 147} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 170 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 88 Chain: "G" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 945 Classifications: {'peptide': 193} Incomplete info: {'truncation_to_alanine': 148} Link IDs: {'PTRANS': 14, 'TRANS': 178} Chain breaks: 4 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 578 Unresolved non-hydrogen angles: 741 Unresolved non-hydrogen dihedrals: 477 Unresolved non-hydrogen chiralities: 62 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 2, 'HIS:plan': 6, 'PHE:plan': 5, 'GLU:plan': 17, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 294 Chain: "X" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 426 Classifications: {'DNA': 21} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 20} Chain: "Y" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 471 Classifications: {'DNA': 23} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 22} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5739 SG CYS D 55 43.572 87.803 58.251 1.00187.00 S ATOM 5755 SG CYS D 58 40.684 86.789 56.482 1.00186.50 S ATOM 5799 SG CYS D 67 43.623 86.075 55.256 1.00198.45 S ATOM 5815 SG CYS D 70 41.299 88.973 54.452 1.00194.96 S ATOM 6485 SG CYS E 55 18.226 31.458 61.849 1.00388.72 S ATOM 6501 SG CYS E 58 19.386 34.024 62.778 1.00384.50 S ATOM 6545 SG CYS E 67 17.483 33.088 65.781 1.00324.74 S ATOM 6561 SG CYS E 70 15.165 33.476 63.024 1.00332.08 S ATOM 7380 SG CYS F 55 68.613 12.947 73.407 1.00115.77 S ATOM 7396 SG CYS F 58 68.887 15.480 74.630 1.00 97.49 S ATOM 7440 SG CYS F 67 69.461 16.970 72.486 1.00131.47 S ATOM 7456 SG CYS F 70 72.318 14.522 72.967 1.00134.38 S Time building chain proxies: 8.65, per 1000 atoms: 0.86 Number of scatterers: 10055 At special positions: 0 Unit cell: (96.32, 100.62, 165.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 3 29.99 S 19 16.00 P 48 15.00 Mg 2 11.99 O 1973 8.00 N 1944 7.00 C 6066 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: 4.46 Conformation dependent library (CDL) restraints added in 3.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 201 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 70 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 67 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 55 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 58 " pdb=" ZN E 201 " pdb="ZN ZN E 201 " - pdb=" SG CYS E 67 " pdb="ZN ZN E 201 " - pdb=" SG CYS E 70 " pdb="ZN ZN E 201 " - pdb=" SG CYS E 55 " pdb="ZN ZN E 201 " - pdb=" SG CYS E 58 " pdb=" ZN F 201 " pdb="ZN ZN F 201 " - pdb=" SG CYS F 67 " pdb="ZN ZN F 201 " - pdb=" SG CYS F 70 " pdb="ZN ZN F 201 " - pdb=" SG CYS F 58 " pdb="ZN ZN F 201 " - pdb=" SG CYS F 55 " Number of angles added : 18 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2540 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 56 helices and 13 sheets defined 46.0% alpha, 12.5% beta 11 base pairs and 42 stacking pairs defined. Time for finding SS restraints: 4.31 Creating SS restraints... Processing helix chain 'A' and resid 36 through 46 Processing helix chain 'A' and resid 55 through 57 No H-bonds generated for 'chain 'A' and resid 55 through 57' Processing helix chain 'A' and resid 101 through 106 Processing helix chain 'A' and resid 115 through 121 Processing helix chain 'A' and resid 125 through 138 removed outlier: 3.680A pdb=" N ARG A 138 " --> pdb=" O ARG A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 162 Processing helix chain 'A' and resid 169 through 203 removed outlier: 3.896A pdb=" N TYR A 178 " --> pdb=" O GLU A 174 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLU A 181 " --> pdb=" O ARG A 177 " (cutoff:3.500A) Proline residue: A 195 - end of helix removed outlier: 3.943A pdb=" N ALA A 203 " --> pdb=" O GLU A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 226 Processing helix chain 'A' and resid 229 through 235 Processing helix chain 'A' and resid 242 through 244 No H-bonds generated for 'chain 'A' and resid 242 through 244' Processing helix chain 'A' and resid 262 through 284 Processing helix chain 'A' and resid 301 through 313 removed outlier: 4.292A pdb=" N ALA A 313 " --> pdb=" O ALA A 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 46 Processing helix chain 'B' and resid 101 through 106 removed outlier: 3.955A pdb=" N GLU B 106 " --> pdb=" O ARG B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 122 removed outlier: 3.762A pdb=" N LEU B 118 " --> pdb=" O PRO B 115 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU B 119 " --> pdb=" O LEU B 116 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU B 122 " --> pdb=" O GLU B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 137 Processing helix chain 'B' and resid 142 through 162 Processing helix chain 'B' and resid 170 through 204 removed outlier: 4.061A pdb=" N GLU B 181 " --> pdb=" O ARG B 177 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA B 184 " --> pdb=" O ASP B 180 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG B 192 " --> pdb=" O ARG B 188 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) Proline residue: B 195 - end of helix Processing helix chain 'B' and resid 221 through 235 removed outlier: 3.692A pdb=" N SER B 228 " --> pdb=" O ALA B 224 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N ALA B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N GLU B 231 " --> pdb=" O ALA B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 244 No H-bonds generated for 'chain 'B' and resid 242 through 244' Processing helix chain 'B' and resid 256 through 259 No H-bonds generated for 'chain 'B' and resid 256 through 259' Processing helix chain 'B' and resid 262 through 284 Processing helix chain 'B' and resid 301 through 313 removed outlier: 4.161A pdb=" N ALA B 313 " --> pdb=" O ALA B 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 15 Processing helix chain 'C' and resid 22 through 34 Processing helix chain 'C' and resid 36 through 47 Processing helix chain 'D' and resid 5 through 16 Processing helix chain 'D' and resid 22 through 33 Processing helix chain 'D' and resid 36 through 46 Processing helix chain 'D' and resid 86 through 95 Processing helix chain 'D' and resid 126 through 128 No H-bonds generated for 'chain 'D' and resid 126 through 128' Processing helix chain 'D' and resid 143 through 152 Processing helix chain 'D' and resid 176 through 178 No H-bonds generated for 'chain 'D' and resid 176 through 178' Processing helix chain 'D' and resid 181 through 189 Processing helix chain 'E' and resid 10 through 16 Processing helix chain 'E' and resid 23 through 34 Processing helix chain 'E' and resid 36 through 49 Processing helix chain 'E' and resid 86 through 95 Processing helix chain 'E' and resid 111 through 113 No H-bonds generated for 'chain 'E' and resid 111 through 113' Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 143 through 158 Processing helix chain 'E' and resid 181 through 189 Processing helix chain 'F' and resid 5 through 16 Processing helix chain 'F' and resid 22 through 34 Processing helix chain 'F' and resid 37 through 46 Processing helix chain 'F' and resid 86 through 95 removed outlier: 3.772A pdb=" N SER F 95 " --> pdb=" O ALA F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 128 removed outlier: 3.863A pdb=" N ARG F 127 " --> pdb=" O GLU F 123 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ARG F 128 " --> pdb=" O GLY F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 159 Processing helix chain 'G' and resid 88 through 91 removed outlier: 3.925A pdb=" N GLU G 91 " --> pdb=" O HIS G 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 88 through 91' Processing helix chain 'G' and resid 93 through 108 Processing helix chain 'G' and resid 112 through 131 Proline residue: G 116 - end of helix Proline residue: G 120 - end of helix Processing helix chain 'G' and resid 135 through 149 removed outlier: 3.516A pdb=" N ARG G 145 " --> pdb=" O TRP G 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 188 Processing helix chain 'G' and resid 191 through 198 Proline residue: G 196 - end of helix Processing helix chain 'G' and resid 206 through 218 Processing helix chain 'G' and resid 222 through 225 removed outlier: 3.941A pdb=" N GLU G 225 " --> pdb=" O ARG G 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 222 through 225' Processing sheet with id= A, first strand: chain 'A' and resid 25 through 29 removed outlier: 6.987A pdb=" N ALA A 317 " --> pdb=" O SER A 26 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N LEU A 28 " --> pdb=" O ALA A 317 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LEU A 319 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU A 290 " --> pdb=" O ILE A 318 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N ALA A 320 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N VAL A 292 " --> pdb=" O ALA A 320 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 78 through 86 removed outlier: 6.667A pdb=" N GLU A 73 " --> pdb=" O LEU A 3 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N LEU A 3 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 209 through 214 removed outlier: 3.613A pdb=" N ASP A 246 " --> pdb=" O GLU A 214 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 332 through 334 Processing sheet with id= E, first strand: chain 'B' and resid 24 through 29 removed outlier: 3.702A pdb=" N ALA B 317 " --> pdb=" O GLY B 24 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N LEU B 290 " --> pdb=" O ILE B 318 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N ALA B 320 " --> pdb=" O LEU B 290 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N VAL B 292 " --> pdb=" O ALA B 320 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 78 through 85 removed outlier: 7.013A pdb=" N GLU B 73 " --> pdb=" O LEU B 3 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N LEU B 3 " --> pdb=" O GLU B 73 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 209 through 214 removed outlier: 3.533A pdb=" N ASP B 246 " --> pdb=" O GLU B 214 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 331 through 334 Processing sheet with id= I, first strand: chain 'D' and resid 79 through 82 removed outlier: 7.396A pdb=" N GLU D 134 " --> pdb=" O LEU D 80 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N VAL D 82 " --> pdb=" O GLU D 134 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N VAL D 136 " --> pdb=" O VAL D 82 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ARG D 162 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N LEU D 137 " --> pdb=" O ARG D 162 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N THR D 164 " --> pdb=" O LEU D 137 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'E' and resid 101 through 104 removed outlier: 3.583A pdb=" N HIS E 103 " --> pdb=" O ALA E 81 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL E 83 " --> pdb=" O HIS E 103 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N GLU E 134 " --> pdb=" O LEU E 80 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL E 82 " --> pdb=" O GLU E 134 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N VAL E 136 " --> pdb=" O VAL E 82 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ARG E 162 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N LEU E 137 " --> pdb=" O ARG E 162 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N THR E 164 " --> pdb=" O LEU E 137 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 101 through 104 Processing sheet with id= L, first strand: chain 'G' and resid 39 through 45 removed outlier: 7.545A pdb=" N VAL G 35 " --> pdb=" O VAL G 19 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL G 19 " --> pdb=" O VAL G 35 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN G 80 " --> pdb=" O GLN G 67 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N TYR G 69 " --> pdb=" O LEU G 78 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N LEU G 78 " --> pdb=" O TYR G 69 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 162 through 164 482 hydrogen bonds defined for protein. 1373 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 27 hydrogen bonds 54 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 42 stacking parallelities Total time for adding SS restraints: 2.94 Time building geometry restraints manager: 4.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3129 1.34 - 1.45: 1455 1.45 - 1.57: 5550 1.57 - 1.69: 94 1.69 - 1.81: 22 Bond restraints: 10250 Sorted by residual: bond pdb=" N3B ANP B 901 " pdb=" PG ANP B 901 " ideal model delta sigma weight residual 1.795 1.629 0.166 2.00e-02 2.50e+03 6.86e+01 bond pdb=" N3B ANP A 901 " pdb=" PG ANP A 901 " ideal model delta sigma weight residual 1.795 1.631 0.164 2.00e-02 2.50e+03 6.73e+01 bond pdb=" O3A ANP B 901 " pdb=" PB ANP B 901 " ideal model delta sigma weight residual 1.700 1.622 0.078 2.00e-02 2.50e+03 1.54e+01 bond pdb=" O3A ANP A 901 " pdb=" PB ANP A 901 " ideal model delta sigma weight residual 1.700 1.622 0.078 2.00e-02 2.50e+03 1.50e+01 bond pdb=" O5' ANP B 901 " pdb=" PA ANP B 901 " ideal model delta sigma weight residual 1.655 1.593 0.062 2.00e-02 2.50e+03 9.63e+00 ... (remaining 10245 not shown) Histogram of bond angle deviations from ideal: 100.33 - 107.13: 530 107.13 - 113.94: 5699 113.94 - 120.74: 4456 120.74 - 127.54: 3337 127.54 - 134.34: 124 Bond angle restraints: 14146 Sorted by residual: angle pdb=" O1B ANP A 901 " pdb=" PB ANP A 901 " pdb=" O3A ANP A 901 " ideal model delta sigma weight residual 103.40 114.41 -11.01 3.00e+00 1.11e-01 1.35e+01 angle pdb=" O1B ANP B 901 " pdb=" PB ANP B 901 " pdb=" O3A ANP B 901 " ideal model delta sigma weight residual 103.40 114.37 -10.97 3.00e+00 1.11e-01 1.34e+01 angle pdb=" PA ANP A 901 " pdb=" O3A ANP A 901 " pdb=" PB ANP A 901 " ideal model delta sigma weight residual 125.41 133.35 -7.94 3.00e+00 1.11e-01 7.01e+00 angle pdb=" PA ANP B 901 " pdb=" O3A ANP B 901 " pdb=" PB ANP B 901 " ideal model delta sigma weight residual 125.41 133.13 -7.72 3.00e+00 1.11e-01 6.61e+00 angle pdb=" CB LYS F 118 " pdb=" CG LYS F 118 " pdb=" CD LYS F 118 " ideal model delta sigma weight residual 111.30 117.18 -5.88 2.30e+00 1.89e-01 6.53e+00 ... (remaining 14141 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 5287 17.95 - 35.89: 440 35.89 - 53.84: 235 53.84 - 71.79: 28 71.79 - 89.73: 10 Dihedral angle restraints: 6000 sinusoidal: 2060 harmonic: 3940 Sorted by residual: dihedral pdb=" CA ALA E 167 " pdb=" C ALA E 167 " pdb=" N TYR E 168 " pdb=" CA TYR E 168 " ideal model delta harmonic sigma weight residual 180.00 161.80 18.20 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA GLU D 133 " pdb=" C GLU D 133 " pdb=" N GLU D 134 " pdb=" CA GLU D 134 " ideal model delta harmonic sigma weight residual 180.00 162.17 17.83 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA ARG D 127 " pdb=" C ARG D 127 " pdb=" N ARG D 128 " pdb=" CA ARG D 128 " ideal model delta harmonic sigma weight residual 180.00 162.86 17.14 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 5997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1505 0.057 - 0.113: 166 0.113 - 0.170: 4 0.170 - 0.227: 0 0.227 - 0.283: 2 Chirality restraints: 1677 Sorted by residual: chirality pdb=" C3' ANP B 901 " pdb=" C2' ANP B 901 " pdb=" C4' ANP B 901 " pdb=" O3' ANP B 901 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" C3' ANP A 901 " pdb=" C2' ANP A 901 " pdb=" C4' ANP A 901 " pdb=" O3' ANP A 901 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CA VAL F 161 " pdb=" N VAL F 161 " pdb=" C VAL F 161 " pdb=" CB VAL F 161 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.15 2.00e-01 2.50e+01 5.98e-01 ... (remaining 1674 not shown) Planarity restraints: 1745 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP E 88 " -0.006 2.00e-02 2.50e+03 1.28e-02 1.63e+00 pdb=" C ASP E 88 " 0.022 2.00e-02 2.50e+03 pdb=" O ASP E 88 " -0.008 2.00e-02 2.50e+03 pdb=" N LEU E 89 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 114 " 0.021 5.00e-02 4.00e+02 3.14e-02 1.57e+00 pdb=" N PRO A 115 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 115 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 115 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 123 " 0.021 5.00e-02 4.00e+02 3.12e-02 1.56e+00 pdb=" N PRO A 124 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 124 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 124 " 0.017 5.00e-02 4.00e+02 ... (remaining 1742 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 66 2.64 - 3.20: 8364 3.20 - 3.77: 14465 3.77 - 4.33: 18066 4.33 - 4.90: 29886 Nonbonded interactions: 70847 Sorted by model distance: nonbonded pdb=" O2G ANP B 901 " pdb="MG MG B 902 " model vdw 2.072 2.170 nonbonded pdb=" OG1 THR B 37 " pdb="MG MG B 902 " model vdw 2.078 2.170 nonbonded pdb=" O1B ANP B 901 " pdb="MG MG B 902 " model vdw 2.115 2.170 nonbonded pdb=" O1B ANP A 901 " pdb="MG MG A 902 " model vdw 2.132 2.170 nonbonded pdb=" O2G ANP A 901 " pdb="MG MG A 902 " model vdw 2.145 2.170 ... (remaining 70842 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 51 or resid 53 through 72 or (resid 73 and (name \ N or name CA or name C or name O or name CB )) or resid 74 through 96 or (resid \ 97 and (name N or name CA or name C or name O or name CB )) or resid 98 through \ 140 or (resid 141 and (name N or name CA or name C or name O or name CB )) or r \ esid 142 through 165 or (resid 166 and (name N or name CA or name C or name O or \ name CB )) or resid 167 through 191 or resid 193 through 197 or resid 199 throu \ gh 341 or resid 901 through 902)) selection = (chain 'B' and (resid 1 through 49 or (resid 50 and (name N or name CA or name C \ or name O or name CB )) or resid 51 through 191 or resid 193 through 197 or res \ id 199 through 285 or (resid 286 and (name N or name CA or name C or name O or n \ ame CB )) or resid 287 through 341 or resid 901 through 902)) } ncs_group { reference = (chain 'D' and (resid 9 through 18 or resid 22 through 71 or resid 77 through 19 \ 4 or resid 201)) selection = (chain 'E' and (resid 9 through 48 or resid 54 through 102 or resid 122 through \ 153 or resid 162 through 194 or resid 201)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.040 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: 13.040 Check model and map are aligned: 0.150 Set scattering table: 0.110 Process input model: 38.700 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.070 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 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 : 0.004 0.166 10250 Z= 0.221 Angle : 0.509 11.006 14146 Z= 0.253 Chirality : 0.036 0.283 1677 Planarity : 0.003 0.031 1745 Dihedral : 17.505 89.732 3460 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.66 % Allowed : 0.00 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.86 (0.23), residues: 1359 helix: 1.80 (0.21), residues: 638 sheet: 0.54 (0.37), residues: 193 loop : -0.96 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 105 HIS 0.003 0.001 HIS A 277 PHE 0.007 0.001 PHE B 6 TYR 0.004 0.001 TYR B 178 ARG 0.003 0.000 ARG A 335 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 174 time to evaluate : 1.088 Fit side-chains revert: symmetry clash REVERT: A 32 ASN cc_start: 0.7231 (m-40) cc_final: 0.6879 (t0) REVERT: A 34 GLN cc_start: 0.7907 (mm-40) cc_final: 0.7380 (mp10) REVERT: A 55 LEU cc_start: 0.8863 (tp) cc_final: 0.8516 (tp) REVERT: B 131 TYR cc_start: 0.8732 (t80) cc_final: 0.8480 (t80) REVERT: F 129 LEU cc_start: 0.8463 (mm) cc_final: 0.8256 (tp) outliers start: 1 outliers final: 0 residues processed: 174 average time/residue: 0.3384 time to fit residues: 74.1958 Evaluate side-chains 96 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 50.0000 chunk 107 optimal weight: 9.9990 chunk 59 optimal weight: 0.7980 chunk 36 optimal weight: 0.0270 chunk 72 optimal weight: 0.0980 chunk 57 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 82 optimal weight: 20.0000 chunk 128 optimal weight: 30.0000 overall best weight: 0.7840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10250 Z= 0.216 Angle : 0.558 12.382 14146 Z= 0.283 Chirality : 0.039 0.160 1677 Planarity : 0.004 0.032 1745 Dihedral : 16.880 87.750 2012 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.81 % Allowed : 11.26 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.23), residues: 1359 helix: 2.39 (0.21), residues: 656 sheet: 0.58 (0.37), residues: 189 loop : -0.99 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 171 HIS 0.005 0.001 HIS A 257 PHE 0.012 0.001 PHE A 259 TYR 0.021 0.002 TYR F 102 ARG 0.011 0.001 ARG F 94 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 89 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 GLU cc_start: 0.8567 (mp0) cc_final: 0.8274 (mp0) REVERT: B 50 GLU cc_start: 0.7482 (mm-30) cc_final: 0.7232 (pm20) REVERT: B 131 TYR cc_start: 0.8831 (t80) cc_final: 0.8472 (t80) REVERT: F 90 TYR cc_start: 0.7361 (OUTLIER) cc_final: 0.6881 (m-80) REVERT: F 129 LEU cc_start: 0.8486 (mm) cc_final: 0.8162 (tt) outliers start: 14 outliers final: 11 residues processed: 96 average time/residue: 0.2545 time to fit residues: 33.4637 Evaluate side-chains 85 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 73 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain F residue 90 TYR Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 161 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 71 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 107 optimal weight: 8.9990 chunk 87 optimal weight: 0.0050 chunk 35 optimal weight: 0.9990 chunk 129 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 128 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 chunk 103 optimal weight: 20.0000 overall best weight: 1.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10250 Z= 0.300 Angle : 0.596 11.176 14146 Z= 0.302 Chirality : 0.040 0.147 1677 Planarity : 0.005 0.042 1745 Dihedral : 16.828 86.471 2012 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.81 % Allowed : 12.75 % Favored : 83.44 % 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: 1.49 (0.23), residues: 1359 helix: 2.57 (0.21), residues: 649 sheet: 0.81 (0.36), residues: 184 loop : -1.04 (0.25), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 295 HIS 0.007 0.002 HIS A 257 PHE 0.024 0.003 PHE A 259 TYR 0.018 0.002 TYR F 102 ARG 0.010 0.001 ARG F 159 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 81 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.8529 (mm-40) cc_final: 0.7912 (mp10) REVERT: B 131 TYR cc_start: 0.8914 (t80) cc_final: 0.8485 (t80) REVERT: F 90 TYR cc_start: 0.7230 (OUTLIER) cc_final: 0.6698 (m-80) REVERT: F 115 ILE cc_start: 0.9233 (mp) cc_final: 0.8912 (mp) REVERT: F 127 ARG cc_start: 0.8704 (ppt170) cc_final: 0.8251 (ppt170) REVERT: F 129 LEU cc_start: 0.8539 (mm) cc_final: 0.8223 (tt) outliers start: 20 outliers final: 13 residues processed: 90 average time/residue: 0.2609 time to fit residues: 32.1811 Evaluate side-chains 76 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 62 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain F residue 90 TYR Chi-restraints excluded: chain F residue 152 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 127 optimal weight: 20.0000 chunk 97 optimal weight: 8.9990 chunk 67 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 chunk 137 optimal weight: 50.0000 chunk 122 optimal weight: 50.0000 chunk 36 optimal weight: 0.0060 chunk 114 optimal weight: 1.9990 overall best weight: 0.8598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 HIS ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10250 Z= 0.201 Angle : 0.514 9.178 14146 Z= 0.261 Chirality : 0.038 0.143 1677 Planarity : 0.004 0.037 1745 Dihedral : 16.642 89.157 2012 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.32 % Allowed : 16.06 % Favored : 81.62 % 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: 1.71 (0.23), residues: 1359 helix: 2.74 (0.21), residues: 651 sheet: 0.82 (0.36), residues: 181 loop : -0.90 (0.25), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 105 HIS 0.005 0.001 HIS A 257 PHE 0.013 0.001 PHE A 259 TYR 0.014 0.001 TYR F 102 ARG 0.006 0.001 ARG F 94 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 75 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.8453 (mm-40) cc_final: 0.7580 (mp10) REVERT: B 131 TYR cc_start: 0.8932 (t80) cc_final: 0.8482 (t80) REVERT: B 312 GLN cc_start: 0.9062 (tm-30) cc_final: 0.8597 (tp40) REVERT: F 90 TYR cc_start: 0.7210 (OUTLIER) cc_final: 0.6764 (m-80) REVERT: F 115 ILE cc_start: 0.9219 (mp) cc_final: 0.8907 (mp) REVERT: F 129 LEU cc_start: 0.8564 (mm) cc_final: 0.8242 (tt) outliers start: 11 outliers final: 8 residues processed: 82 average time/residue: 0.2436 time to fit residues: 27.9065 Evaluate side-chains 75 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 66 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain F residue 90 TYR Chi-restraints excluded: chain F residue 152 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 77 optimal weight: 20.0000 chunk 1 optimal weight: 2.9990 chunk 102 optimal weight: 40.0000 chunk 56 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 94 optimal weight: 40.0000 chunk 0 optimal weight: 2.9990 chunk 70 optimal weight: 8.9990 chunk 123 optimal weight: 50.0000 chunk 34 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.4176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.051 10250 Z= 0.527 Angle : 0.741 10.460 14146 Z= 0.377 Chirality : 0.044 0.146 1677 Planarity : 0.006 0.064 1745 Dihedral : 17.049 95.365 2012 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.97 % Allowed : 17.05 % Favored : 78.97 % 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: 1.16 (0.23), residues: 1359 helix: 2.37 (0.21), residues: 648 sheet: 0.20 (0.37), residues: 183 loop : -1.11 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP A 295 HIS 0.027 0.005 HIS A 283 PHE 0.038 0.003 PHE A 259 TYR 0.018 0.002 TYR A 150 ARG 0.009 0.001 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 68 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.8441 (mm-40) cc_final: 0.7606 (mp10) REVERT: A 284 HIS cc_start: 0.7808 (OUTLIER) cc_final: 0.7123 (t-170) REVERT: B 312 GLN cc_start: 0.9065 (tm-30) cc_final: 0.8599 (tm-30) REVERT: F 90 TYR cc_start: 0.7298 (OUTLIER) cc_final: 0.6840 (m-80) REVERT: F 115 ILE cc_start: 0.9184 (mp) cc_final: 0.8849 (mp) REVERT: F 129 LEU cc_start: 0.8663 (mm) cc_final: 0.8307 (tp) outliers start: 21 outliers final: 15 residues processed: 80 average time/residue: 0.2608 time to fit residues: 28.6755 Evaluate side-chains 78 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 61 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain F residue 90 TYR Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 156 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 123 optimal weight: 50.0000 chunk 27 optimal weight: 0.5980 chunk 80 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 137 optimal weight: 0.0030 chunk 114 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 72 optimal weight: 3.9990 chunk 132 optimal weight: 50.0000 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 HIS ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10250 Z= 0.169 Angle : 0.520 10.617 14146 Z= 0.262 Chirality : 0.037 0.140 1677 Planarity : 0.003 0.046 1745 Dihedral : 16.705 87.477 2012 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.32 % Allowed : 19.04 % Favored : 78.64 % 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: 1.65 (0.23), residues: 1359 helix: 2.77 (0.21), residues: 653 sheet: 0.58 (0.37), residues: 191 loop : -0.98 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 105 HIS 0.005 0.001 HIS B 284 PHE 0.008 0.001 PHE A 259 TYR 0.011 0.001 TYR F 102 ARG 0.009 0.001 ARG F 94 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 70 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.8411 (mm-40) cc_final: 0.7531 (mp10) REVERT: B 131 TYR cc_start: 0.8946 (t80) cc_final: 0.8344 (t80) REVERT: B 312 GLN cc_start: 0.9009 (tm-30) cc_final: 0.8547 (tm-30) REVERT: F 90 TYR cc_start: 0.7288 (OUTLIER) cc_final: 0.6816 (m-80) REVERT: F 115 ILE cc_start: 0.9145 (mp) cc_final: 0.8819 (mp) REVERT: F 129 LEU cc_start: 0.8587 (mm) cc_final: 0.8265 (tp) outliers start: 11 outliers final: 10 residues processed: 77 average time/residue: 0.2656 time to fit residues: 27.9626 Evaluate side-chains 78 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 67 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain F residue 90 TYR Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 152 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 15 optimal weight: 0.8980 chunk 78 optimal weight: 50.0000 chunk 100 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 136 optimal weight: 20.0000 chunk 85 optimal weight: 2.9990 chunk 83 optimal weight: 40.0000 chunk 63 optimal weight: 2.9990 chunk 84 optimal weight: 40.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 284 HIS ** B 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.4547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 10250 Z= 0.552 Angle : 0.732 9.588 14146 Z= 0.371 Chirality : 0.044 0.147 1677 Planarity : 0.005 0.068 1745 Dihedral : 16.987 93.430 2012 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 4.30 % Allowed : 18.38 % Favored : 77.32 % 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: 1.24 (0.23), residues: 1359 helix: 2.46 (0.21), residues: 649 sheet: 0.22 (0.37), residues: 183 loop : -1.12 (0.25), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 105 HIS 0.011 0.004 HIS B 277 PHE 0.037 0.003 PHE A 259 TYR 0.017 0.002 TYR A 150 ARG 0.020 0.001 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 63 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.8461 (mm-40) cc_final: 0.7672 (mp10) REVERT: B 39 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8709 (tt) REVERT: B 312 GLN cc_start: 0.9040 (tm-30) cc_final: 0.8560 (tm-30) REVERT: F 90 TYR cc_start: 0.7385 (OUTLIER) cc_final: 0.6878 (m-80) REVERT: F 115 ILE cc_start: 0.9117 (mp) cc_final: 0.8769 (tt) REVERT: F 129 LEU cc_start: 0.8708 (mm) cc_final: 0.8316 (tp) outliers start: 23 outliers final: 16 residues processed: 80 average time/residue: 0.2645 time to fit residues: 29.2059 Evaluate side-chains 79 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 61 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain F residue 90 TYR Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 152 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 54 optimal weight: 0.0670 chunk 81 optimal weight: 30.0000 chunk 41 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 87 optimal weight: 0.0070 chunk 93 optimal weight: 50.0000 chunk 67 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 107 optimal weight: 7.9990 chunk 124 optimal weight: 50.0000 chunk 131 optimal weight: 50.0000 overall best weight: 0.5336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 HIS ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.4518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10250 Z= 0.171 Angle : 0.529 10.780 14146 Z= 0.267 Chirality : 0.037 0.143 1677 Planarity : 0.004 0.049 1745 Dihedral : 16.729 89.826 2012 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.81 % Allowed : 19.37 % Favored : 77.81 % 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: 1.63 (0.23), residues: 1359 helix: 2.77 (0.21), residues: 653 sheet: 0.45 (0.36), residues: 204 loop : -1.01 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 105 HIS 0.011 0.001 HIS B 284 PHE 0.009 0.001 PHE A 259 TYR 0.008 0.001 TYR B 178 ARG 0.007 0.001 ARG F 94 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 68 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.8420 (mm-40) cc_final: 0.7619 (mp10) REVERT: B 131 TYR cc_start: 0.8948 (t80) cc_final: 0.8342 (t80) REVERT: B 312 GLN cc_start: 0.8997 (tm-30) cc_final: 0.8507 (tm-30) REVERT: F 90 TYR cc_start: 0.7296 (OUTLIER) cc_final: 0.6816 (m-80) REVERT: F 115 ILE cc_start: 0.9096 (mp) cc_final: 0.8700 (tt) REVERT: F 129 LEU cc_start: 0.8617 (mm) cc_final: 0.8286 (tp) outliers start: 14 outliers final: 11 residues processed: 76 average time/residue: 0.2538 time to fit residues: 26.7927 Evaluate side-chains 79 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 67 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain F residue 90 TYR Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 152 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 50.0000 chunk 127 optimal weight: 30.0000 chunk 131 optimal weight: 50.0000 chunk 76 optimal weight: 7.9990 chunk 55 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 120 optimal weight: 8.9990 chunk 83 optimal weight: 40.0000 chunk 134 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.5149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.092 10250 Z= 0.864 Angle : 0.960 11.998 14146 Z= 0.484 Chirality : 0.051 0.188 1677 Planarity : 0.007 0.092 1745 Dihedral : 17.377 95.349 2012 Min Nonbonded Distance : 1.719 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.75 % Favored : 94.18 % Rotamer: Outliers : 4.47 % Allowed : 18.05 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.23), residues: 1359 helix: 2.02 (0.21), residues: 637 sheet: -0.21 (0.36), residues: 202 loop : -1.13 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP A 105 HIS 0.018 0.005 HIS A 283 PHE 0.053 0.005 PHE A 259 TYR 0.029 0.003 TYR A 150 ARG 0.016 0.001 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 60 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 39 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8736 (tt) REVERT: F 90 TYR cc_start: 0.7475 (OUTLIER) cc_final: 0.6941 (m-80) REVERT: F 115 ILE cc_start: 0.9109 (mp) cc_final: 0.8733 (tt) REVERT: F 129 LEU cc_start: 0.8776 (mm) cc_final: 0.8257 (tp) outliers start: 24 outliers final: 18 residues processed: 77 average time/residue: 0.2793 time to fit residues: 29.9404 Evaluate side-chains 77 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 57 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain F residue 90 TYR Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 152 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 82 optimal weight: 9.9990 chunk 63 optimal weight: 0.5980 chunk 93 optimal weight: 50.0000 chunk 141 optimal weight: 1.9990 chunk 130 optimal weight: 20.0000 chunk 112 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 87 optimal weight: 9.9990 chunk 69 optimal weight: 6.9990 chunk 89 optimal weight: 9.9990 chunk 120 optimal weight: 1.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 284 HIS B 284 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.5079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10250 Z= 0.316 Angle : 0.615 10.845 14146 Z= 0.310 Chirality : 0.040 0.150 1677 Planarity : 0.004 0.074 1745 Dihedral : 17.092 86.866 2012 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.65 % Allowed : 19.87 % Favored : 77.48 % 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: 1.20 (0.23), residues: 1359 helix: 2.45 (0.21), residues: 646 sheet: 0.01 (0.35), residues: 209 loop : -1.10 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 105 HIS 0.010 0.002 HIS B 284 PHE 0.021 0.002 PHE A 259 TYR 0.017 0.002 TYR B 131 ARG 0.007 0.001 ARG F 94 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 62 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 39 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8706 (tt) REVERT: B 131 TYR cc_start: 0.8959 (t80) cc_final: 0.8595 (t80) REVERT: B 312 GLN cc_start: 0.9060 (tm-30) cc_final: 0.8548 (tm-30) REVERT: F 90 TYR cc_start: 0.7380 (OUTLIER) cc_final: 0.6813 (m-80) REVERT: F 115 ILE cc_start: 0.9090 (mp) cc_final: 0.8624 (tt) REVERT: F 129 LEU cc_start: 0.8632 (mm) cc_final: 0.8214 (tp) outliers start: 13 outliers final: 10 residues processed: 72 average time/residue: 0.2500 time to fit residues: 24.9923 Evaluate side-chains 72 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 60 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain F residue 90 TYR Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 152 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 34 optimal weight: 3.9990 chunk 103 optimal weight: 30.0000 chunk 16 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 112 optimal weight: 0.3980 chunk 47 optimal weight: 0.8980 chunk 115 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 99 optimal weight: 20.0000 chunk 6 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.144815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.103066 restraints weight = 54463.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.099805 restraints weight = 23945.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.101475 restraints weight = 16782.302| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3497 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3497 r_free = 0.3497 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3497 r_free = 0.3497 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3497 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.5083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10250 Z= 0.186 Angle : 0.560 11.013 14146 Z= 0.281 Chirality : 0.038 0.139 1677 Planarity : 0.004 0.053 1745 Dihedral : 16.834 82.317 2012 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.48 % Allowed : 20.53 % Favored : 76.99 % 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: 1.51 (0.23), residues: 1359 helix: 2.74 (0.21), residues: 652 sheet: 0.15 (0.36), residues: 204 loop : -1.04 (0.26), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 105 HIS 0.010 0.002 HIS B 284 PHE 0.010 0.001 PHE A 259 TYR 0.016 0.001 TYR B 131 ARG 0.011 0.001 ARG F 94 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1994.08 seconds wall clock time: 36 minutes 41.16 seconds (2201.16 seconds total)